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comparison plink2.xml @ 0:46f45544839f draft

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author blankenberg
date Wed, 25 Nov 2020 01:57:54 +0000
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children 2a8c426ab5bc
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-1:000000000000 0:46f45544839f
1 <tool id="plink2" name="PLINK 2" version="2.00a2.3">
2 <requirements>
3 <requirement type="package" version="2.00a2.3">plink</requirement>
4 </requirements>
5 <code file="plink_code_file.py" />
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <version_command>plink2 --version</version_command>
10 <command><![CDATA[
11 plink2
12
13 #if str($CONDITIONAL_pfile.CONDITIONAL_SELECT_pfile) == "set":
14 --pfile
15
16
17 #if $str($CONDITIONAL_pfile.pfile_MOD_0_0):
18 '${CONDITIONAL_pfile.pfile_MOD_0_0}'
19 #end if
20
21 #if $str($CONDITIONAL_pfile.pfile_MOD_1_0):
22 '${CONDITIONAL_pfile.pfile_MOD_1_0}'
23 #end if
24
25 #end if
26
27 #if str($CONDITIONAL_pgen.CONDITIONAL_SELECT_pgen) == "set":
28 --pgen
29
30
31 #if $CONDITIONAL_pgen.pgen_MOD_0_0:
32 '${CONDITIONAL_pgen.pgen_MOD_0_0}'
33 #end if
34
35 #end if
36
37 #if str($CONDITIONAL_pvar.CONDITIONAL_SELECT_pvar) == "set":
38 --pvar
39
40
41 #if $CONDITIONAL_pvar.pvar_MOD_0_0:
42 '${CONDITIONAL_pvar.pvar_MOD_0_0}'
43 #end if
44
45 #end if
46
47 #if str($CONDITIONAL_psam.CONDITIONAL_SELECT_psam) == "set":
48 --psam
49
50
51 #if $CONDITIONAL_psam.psam_MOD_0_0:
52 '${CONDITIONAL_psam.psam_MOD_0_0}'
53 #end if
54
55 #end if
56
57 #if str($CONDITIONAL_bpfile.CONDITIONAL_SELECT_bpfile) == "set":
58 --bpfile
59
60
61 #if $str($CONDITIONAL_bpfile.bpfile_MOD_0_0):
62 '${CONDITIONAL_bpfile.bpfile_MOD_0_0}'
63 #end if
64
65 #if $str($CONDITIONAL_bpfile.bpfile_MOD_1_0):
66 '${CONDITIONAL_bpfile.bpfile_MOD_1_0}'
67 #end if
68
69 #end if
70
71 #if str($CONDITIONAL_keep_autoconv.CONDITIONAL_SELECT_keep_autoconv) == "set":
72 --keep-autoconv
73
74
75 #end if
76
77 #if str($CONDITIONAL_no_fid.CONDITIONAL_SELECT_no_fid) == "set":
78 --no-fid
79
80
81 #end if
82
83 #if str($CONDITIONAL_no_parents.CONDITIONAL_SELECT_no_parents) == "set":
84 --no-parents
85
86
87 #end if
88
89 #if str($CONDITIONAL_no_sex.CONDITIONAL_SELECT_no_sex) == "set":
90 --no-sex
91
92
93 #end if
94
95 #if str($CONDITIONAL_vcf.CONDITIONAL_SELECT_vcf) == "set":
96 --vcf
97
98
99 #if $CONDITIONAL_vcf.vcf_MOD_0_0:
100 '${CONDITIONAL_vcf.vcf_MOD_0_0}'
101 #end if
102
103 #if $str($CONDITIONAL_vcf.vcf_MOD_1_0):
104 '${CONDITIONAL_vcf.vcf_MOD_1_0}'
105 #end if
106
107 #end if
108
109 #if str($CONDITIONAL_bcf.CONDITIONAL_SELECT_bcf) == "set":
110 --bcf
111
112
113 #if $CONDITIONAL_bcf.bcf_MOD_0_0:
114 '${CONDITIONAL_bcf.bcf_MOD_0_0}'
115 #end if
116
117 #if $str($CONDITIONAL_bcf.bcf_MOD_1_0):
118 '${CONDITIONAL_bcf.bcf_MOD_1_0}'
119 #end if
120
121 #end if
122
123 #if str($CONDITIONAL_bgen.CONDITIONAL_SELECT_bgen) == "set":
124 --bgen
125
126
127 #if $CONDITIONAL_bgen.bgen_MOD_0_0:
128 '${CONDITIONAL_bgen.bgen_MOD_0_0}'
129 #end if
130
131 #if $str($CONDITIONAL_bgen.bgen_MOD_1_0):
132 '${CONDITIONAL_bgen.bgen_MOD_1_0}'
133 #end if
134
135 #if $str($CONDITIONAL_bgen.bgen_MOD_2_0):
136 '${CONDITIONAL_bgen.bgen_MOD_2_0}'
137 #end if
138
139 #end if
140
141 #if str($CONDITIONAL_gen.CONDITIONAL_SELECT_gen) == "set":
142 --gen
143
144
145 #if $CONDITIONAL_gen.gen_MOD_0_0:
146 '${CONDITIONAL_gen.gen_MOD_0_0}'
147 #end if
148
149 #if $str($CONDITIONAL_gen.gen_MOD_1_0):
150 '${CONDITIONAL_gen.gen_MOD_1_0}'
151 #end if
152
153 #end if
154
155 #if str($CONDITIONAL_sample.CONDITIONAL_SELECT_sample) == "set":
156 --sample
157
158
159 #if $CONDITIONAL_sample.sample_MOD_0_0:
160 '${CONDITIONAL_sample.sample_MOD_0_0}'
161 #end if
162
163 #end if
164
165 #if str($CONDITIONAL_haps.CONDITIONAL_SELECT_haps) == "set":
166 --haps
167
168
169 #if $CONDITIONAL_haps.haps_MOD_0_0:
170 '${CONDITIONAL_haps.haps_MOD_0_0}'
171 #end if
172
173 #if $str($CONDITIONAL_haps.CONDITIONAL_haps_MOD_1.CONDITIONAL_SELECT_haps_MOD_1) == 'from_list'
174 '${CONDITIONAL_haps.CONDITIONAL_haps_MOD_1.haps_MOD_1}'
175 #end if
176
177
178 #end if
179
180 #if str($CONDITIONAL_legend.CONDITIONAL_SELECT_legend) == "set":
181 --legend
182
183
184 #if $CONDITIONAL_legend.legend_MOD_0_0:
185 '${CONDITIONAL_legend.legend_MOD_0_0}'
186 #end if
187
188 #if $str($CONDITIONAL_legend.legend_MOD_1_0):
189 '${CONDITIONAL_legend.legend_MOD_1_0}'
190 #end if
191
192 #end if
193
194 #if str($CONDITIONAL_map.CONDITIONAL_SELECT_map) == "set":
195 --map
196
197
198 #if $CONDITIONAL_map.map_MOD_0_0:
199 '${CONDITIONAL_map.map_MOD_0_0}'
200 #end if
201
202 #end if
203
204 #if str($CONDITIONAL_import_dosage.CONDITIONAL_SELECT_import_dosage) == "set":
205 --import-dosage
206
207
208 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_0_0):
209 '${CONDITIONAL_import_dosage.import_dosage_MOD_0_0}'
210 #end if
211
212 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_1_0):
213 '${CONDITIONAL_import_dosage.import_dosage_MOD_1_0}'
214 #end if
215
216 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_2_0):
217 '${CONDITIONAL_import_dosage.import_dosage_MOD_2_0}'
218 #end if
219
220 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_3_0):
221 '${CONDITIONAL_import_dosage.import_dosage_MOD_3_0}'
222 #end if
223
224 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_4_0):
225 '${CONDITIONAL_import_dosage.import_dosage_MOD_4_0}'
226 #end if
227
228 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_5_0):
229 '${CONDITIONAL_import_dosage.import_dosage_MOD_5_0}'
230 #end if
231
232 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_6_0):
233 '${CONDITIONAL_import_dosage.import_dosage_MOD_6_0}'
234 #end if
235
236 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_7_0):
237 '${CONDITIONAL_import_dosage.import_dosage_MOD_7_0}'
238 #end if
239
240 #if $str($CONDITIONAL_import_dosage.CONDITIONAL_import_dosage_MOD_8.CONDITIONAL_SELECT_import_dosage_MOD_8) == 'from_list'
241 '${CONDITIONAL_import_dosage.CONDITIONAL_import_dosage_MOD_8.import_dosage_MOD_8}'
242 #end if
243
244
245 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_9_0):
246 '${CONDITIONAL_import_dosage.import_dosage_MOD_9_0}'
247 #end if
248
249 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_10_0):
250 '${CONDITIONAL_import_dosage.import_dosage_MOD_10_0}'
251 #end if
252
253 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_11_0):
254 '${CONDITIONAL_import_dosage.import_dosage_MOD_11_0}'
255 #end if
256
257 #end if
258
259 #if str($CONDITIONAL_dummy.CONDITIONAL_SELECT_dummy) == "set":
260 --dummy
261
262
263 #if $str($CONDITIONAL_dummy.dummy_MOD_0_0):
264 '${CONDITIONAL_dummy.dummy_MOD_0_0}'
265 #end if
266
267 #if $str($CONDITIONAL_dummy.dummy_MOD_1_0):
268 '${CONDITIONAL_dummy.dummy_MOD_1_0}'
269 #end if
270
271 #if $str($CONDITIONAL_dummy.dummy_MOD_2_0):
272 '${CONDITIONAL_dummy.dummy_MOD_2_0}'
273 #end if
274
275 #if $str($CONDITIONAL_dummy.dummy_MOD_3_0):
276 '${CONDITIONAL_dummy.dummy_MOD_3_0}'
277 #end if
278
279 #if $str($CONDITIONAL_dummy.CONDITIONAL_dummy_MOD_4.CONDITIONAL_SELECT_dummy_MOD_4) == 'from_list'
280 '${CONDITIONAL_dummy.CONDITIONAL_dummy_MOD_4.dummy_MOD_4}'
281 #end if
282
283
284 #if $str($CONDITIONAL_dummy.dummy_MOD_5_0):
285 '${CONDITIONAL_dummy.dummy_MOD_5_0}'
286 #end if
287
288 #if $str($CONDITIONAL_dummy.dummy_MOD_6_0):
289 '${CONDITIONAL_dummy.dummy_MOD_6_0}'
290 #end if
291
292 #if $str($CONDITIONAL_dummy.dummy_MOD_7_0):
293 '${CONDITIONAL_dummy.dummy_MOD_7_0}'
294 #end if
295
296 #end if
297
298 #if str($CONDITIONAL_fa.CONDITIONAL_SELECT_fa) == "set":
299 --fa
300
301
302 #if $CONDITIONAL_fa.fa_MOD_0_0:
303 '${CONDITIONAL_fa.fa_MOD_0_0}'
304 #end if
305
306 #end if
307
308 #if str($CONDITIONAL_rm_dup.CONDITIONAL_SELECT_rm_dup) == "set":
309 --rm-dup
310
311
312 #if $str($CONDITIONAL_rm_dup.rm_dup_MOD_0_0):
313 '${CONDITIONAL_rm_dup.rm_dup_MOD_0_0}'
314 #end if
315
316 #if $str($CONDITIONAL_rm_dup.rm_dup_MOD_1_0):
317 '${CONDITIONAL_rm_dup.rm_dup_MOD_1_0}'
318 #end if
319
320 #end if
321
322 #if str($CONDITIONAL_make_pgen.CONDITIONAL_SELECT_make_pgen) == "set":
323 --make-pgen
324
325
326 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_0_0):
327 '${CONDITIONAL_make_pgen.make_pgen_MOD_0_0}'
328 #end if
329
330 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_1_0):
331 '${CONDITIONAL_make_pgen.make_pgen_MOD_1_0}'
332 #end if
333
334 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_2_0):
335 '${CONDITIONAL_make_pgen.make_pgen_MOD_2_0}'
336 #end if
337
338 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_3_0):
339 '${CONDITIONAL_make_pgen.make_pgen_MOD_3_0}'
340 #end if
341
342 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_4_0):
343 '${CONDITIONAL_make_pgen.make_pgen_MOD_4_0}'
344 #end if
345
346 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_5_0):
347 '${CONDITIONAL_make_pgen.make_pgen_MOD_5_0}'
348 #end if
349
350 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_6_0):
351 '${CONDITIONAL_make_pgen.make_pgen_MOD_6_0}'
352 #end if
353
354 #end if
355
356 #if str($CONDITIONAL_make_bpgen.CONDITIONAL_SELECT_make_bpgen) == "set":
357 --make-bpgen
358
359
360 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_0_0):
361 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_0_0}'
362 #end if
363
364 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_1_0):
365 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_1_0}'
366 #end if
367
368 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_2_0):
369 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_2_0}'
370 #end if
371
372 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_3_0):
373 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_3_0}'
374 #end if
375
376 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_4_0):
377 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_4_0}'
378 #end if
379
380 #end if
381
382 #if str($CONDITIONAL_make_bed.CONDITIONAL_SELECT_make_bed) == "set":
383 --make-bed
384
385
386 #if $str($CONDITIONAL_make_bed.make_bed_MOD_0_0):
387 '${CONDITIONAL_make_bed.make_bed_MOD_0_0}'
388 #end if
389
390 #if $str($CONDITIONAL_make_bed.make_bed_MOD_1_0):
391 '${CONDITIONAL_make_bed.make_bed_MOD_1_0}'
392 #end if
393
394 #end if
395
396 #if str($CONDITIONAL_make_just_pvar.CONDITIONAL_SELECT_make_just_pvar) == "set":
397 --make-just-pvar
398
399
400 #if $str($CONDITIONAL_make_just_pvar.make_just_pvar_MOD_0_0):
401 '${CONDITIONAL_make_just_pvar.make_just_pvar_MOD_0_0}'
402 #end if
403
404 #if $str($CONDITIONAL_make_just_pvar.make_just_pvar_MOD_1_0):
405 '${CONDITIONAL_make_just_pvar.make_just_pvar_MOD_1_0}'
406 #end if
407
408 #end if
409
410 #if str($CONDITIONAL_make_just_psam.CONDITIONAL_SELECT_make_just_psam) == "set":
411 --make-just-psam
412
413
414 #if $str($CONDITIONAL_make_just_psam.make_just_psam_MOD_0_0):
415 '${CONDITIONAL_make_just_psam.make_just_psam_MOD_0_0}'
416 #end if
417
418 #end if
419
420 #if str($CONDITIONAL_make_just_bim.CONDITIONAL_SELECT_make_just_bim) == "set":
421 --make-just-bim
422
423
424 #if $str($CONDITIONAL_make_just_bim.make_just_bim_MOD_0_0):
425 '${CONDITIONAL_make_just_bim.make_just_bim_MOD_0_0}'
426 #end if
427
428 #end if
429
430 ${make_just_fam}
431
432 #if str($CONDITIONAL_export.CONDITIONAL_SELECT_export) == "set":
433 --export
434
435
436 #if $str($CONDITIONAL_export.export_MOD_0_0):
437 '${CONDITIONAL_export.export_MOD_0_0}'
438 #end if
439
440 #if $str($CONDITIONAL_export.CONDITIONAL_export_MOD_1.CONDITIONAL_SELECT_export_MOD_1) == 'from_list'
441 '${CONDITIONAL_export.CONDITIONAL_export_MOD_1.export_MOD_1}'
442 #end if
443
444
445 #if $str($CONDITIONAL_export.export_MOD_2_0):
446 '${CONDITIONAL_export.export_MOD_2_0}'
447 #end if
448
449 #if $str($CONDITIONAL_export.export_MOD_3_0):
450 '${CONDITIONAL_export.export_MOD_3_0}'
451 #end if
452
453 #if $str($CONDITIONAL_export.export_MOD_4_0):
454 '${CONDITIONAL_export.export_MOD_4_0}'
455 #end if
456
457 #if $str($CONDITIONAL_export.export_MOD_5_0):
458 '${CONDITIONAL_export.export_MOD_5_0}'
459 #end if
460
461 #if $str($CONDITIONAL_export.export_MOD_6_0):
462 '${CONDITIONAL_export.export_MOD_6_0}'
463 #end if
464
465 #if $str($CONDITIONAL_export.export_MOD_7_0):
466 '${CONDITIONAL_export.export_MOD_7_0}'
467 #end if
468
469 #if $str($CONDITIONAL_export.export_MOD_8_0):
470 '${CONDITIONAL_export.export_MOD_8_0}'
471 #end if
472
473 #if $str($CONDITIONAL_export.export_MOD_9_0):
474 '${CONDITIONAL_export.export_MOD_9_0}'
475 #end if
476
477 #if $str($CONDITIONAL_export.export_MOD_10_0):
478 '${CONDITIONAL_export.export_MOD_10_0}'
479 #end if
480
481 #end if
482
483 #if str($CONDITIONAL_freq.CONDITIONAL_SELECT_freq) == "set":
484 --freq
485
486
487 #if $str($CONDITIONAL_freq.freq_MOD_0_0):
488 '${CONDITIONAL_freq.freq_MOD_0_0}'
489 #end if
490
491 #if $str($CONDITIONAL_freq.freq_MOD_1_0):
492 '${CONDITIONAL_freq.freq_MOD_1_0}'
493 #end if
494
495 #if $str($CONDITIONAL_freq.freq_MOD_2_0):
496 '${CONDITIONAL_freq.freq_MOD_2_0}'
497 #end if
498
499 #if $str($CONDITIONAL_freq.freq_MOD_3_0):
500 '${CONDITIONAL_freq.freq_MOD_3_0}'
501 #end if
502
503 #end if
504
505 #if str($CONDITIONAL_geno_counts.CONDITIONAL_SELECT_geno_counts) == "set":
506 --geno-counts
507
508
509 #if $str($CONDITIONAL_geno_counts.geno_counts_MOD_0_0):
510 '${CONDITIONAL_geno_counts.geno_counts_MOD_0_0}'
511 #end if
512
513 #if $str($CONDITIONAL_geno_counts.geno_counts_MOD_1_0):
514 '${CONDITIONAL_geno_counts.geno_counts_MOD_1_0}'
515 #end if
516
517 #end if
518
519 #if str($CONDITIONAL_sample_counts.CONDITIONAL_SELECT_sample_counts) == "set":
520 --sample-counts
521
522
523 #if $str($CONDITIONAL_sample_counts.sample_counts_MOD_0_0):
524 '${CONDITIONAL_sample_counts.sample_counts_MOD_0_0}'
525 #end if
526
527 #if $str($CONDITIONAL_sample_counts.sample_counts_MOD_1_0):
528 '${CONDITIONAL_sample_counts.sample_counts_MOD_1_0}'
529 #end if
530
531 #end if
532
533 #if str($CONDITIONAL_missing.CONDITIONAL_SELECT_missing) == "set":
534 --missing
535
536
537 #if $str($CONDITIONAL_missing.missing_MOD_0_0):
538 '${CONDITIONAL_missing.missing_MOD_0_0}'
539 #end if
540
541 #if $str($CONDITIONAL_missing.CONDITIONAL_missing_MOD_1.CONDITIONAL_SELECT_missing_MOD_1) == 'from_list'
542 '${CONDITIONAL_missing.CONDITIONAL_missing_MOD_1.missing_MOD_1}'
543 #end if
544
545
546 #if $str($CONDITIONAL_missing.missing_MOD_2_0):
547 '${CONDITIONAL_missing.missing_MOD_2_0}'
548 #end if
549
550 #if $str($CONDITIONAL_missing.missing_MOD_3_0):
551 '${CONDITIONAL_missing.missing_MOD_3_0}'
552 #end if
553
554 #end if
555
556 #if str($CONDITIONAL_hardy.CONDITIONAL_SELECT_hardy) == "set":
557 --hardy
558
559
560 #if $str($CONDITIONAL_hardy.hardy_MOD_0_0):
561 '${CONDITIONAL_hardy.hardy_MOD_0_0}'
562 #end if
563
564 #if $str($CONDITIONAL_hardy.hardy_MOD_1_0):
565 '${CONDITIONAL_hardy.hardy_MOD_1_0}'
566 #end if
567
568 #if $str($CONDITIONAL_hardy.hardy_MOD_2_0):
569 '${CONDITIONAL_hardy.hardy_MOD_2_0}'
570 #end if
571
572 #if $str($CONDITIONAL_hardy.hardy_MOD_3_0):
573 '${CONDITIONAL_hardy.hardy_MOD_3_0}'
574 #end if
575
576 #end if
577
578 #if str($CONDITIONAL_indep_pairwise.CONDITIONAL_SELECT_indep_pairwise) == "set":
579 --indep-pairwise
580
581
582 #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_0_0):
583 '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_0_0}'
584 #end if
585
586 #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_1_0):
587 '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_1_0}'
588 #end if
589
590 #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_2_0):
591 '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_2_0}'
592 #end if
593
594 #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_3_0):
595 '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_3_0}'
596 #end if
597
598 #end if
599
600 #if str($CONDITIONAL_ld.CONDITIONAL_SELECT_ld) == "set":
601 --ld
602
603
604 #if $str($CONDITIONAL_ld.ld_MOD_0_0):
605 '${CONDITIONAL_ld.ld_MOD_0_0}'
606 #end if
607
608 #if $str($CONDITIONAL_ld.ld_MOD_1_0):
609 '${CONDITIONAL_ld.ld_MOD_1_0}'
610 #end if
611
612 #if $str($CONDITIONAL_ld.ld_MOD_2_0):
613 '${CONDITIONAL_ld.ld_MOD_2_0}'
614 #end if
615
616 #if $str($CONDITIONAL_ld.ld_MOD_3_0):
617 '${CONDITIONAL_ld.ld_MOD_3_0}'
618 #end if
619
620 #end if
621
622 #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_OVERLOADED_SELECT_sample_diff) == "form_0":
623 #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_SELECT_sample_diff) == "set":
624 --sample-diff
625
626 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0):
627 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0}'
628 #end if
629 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.CONDITIONAL_SELECT_sample_diff_MOD_1) == 'from_list'
630 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.sample_diff_MOD_1}'
631 #end if
632
633 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0):
634 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0}'
635 #end if
636 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.CONDITIONAL_SELECT_sample_diff_MOD_3) == 'from_list'
637 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.sample_diff_MOD_3}'
638 #end if
639
640 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0):
641 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0}'
642 #end if
643 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0):
644 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0}'
645 #end if
646 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0):
647 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0}'
648 #end if
649 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0):
650 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0}'
651 #end if
652 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_8.CONDITIONAL_SELECT_sample_diff_MOD_8) == 'from_list'
653 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_8.sample_diff_MOD_8}'
654 #end if
655
656 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_9_0):
657 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_9_0}'
658 #end if
659 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_10_0):
660 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_10_0}'
661 #end if
662 #end if
663 #end if
664
665 #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_OVERLOADED_SELECT_sample_diff) == "form_1":
666 #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_SELECT_sample_diff) == "set":
667 --sample-diff
668
669 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0):
670 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0}'
671 #end if
672 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.CONDITIONAL_SELECT_sample_diff_MOD_1) == 'from_list'
673 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.sample_diff_MOD_1}'
674 #end if
675
676 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0):
677 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0}'
678 #end if
679 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.CONDITIONAL_SELECT_sample_diff_MOD_3) == 'from_list'
680 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.sample_diff_MOD_3}'
681 #end if
682
683 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0):
684 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0}'
685 #end if
686 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0):
687 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0}'
688 #end if
689 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0):
690 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0}'
691 #end if
692 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0):
693 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0}'
694 #end if
695 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_8_0):
696 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_8_0}'
697 #end if
698 #end if
699 #end if
700
701 #if str($CONDITIONAL_make_king.CONDITIONAL_SELECT_make_king) == "set":
702 --make-king
703
704
705 #if $str($CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_0.CONDITIONAL_SELECT_make_king_MOD_0) == 'from_list'
706 '${CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_0.make_king_MOD_0}'
707 #end if
708
709
710 #if $str($CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_1.CONDITIONAL_SELECT_make_king_MOD_1) == 'from_list'
711 '${CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_1.make_king_MOD_1}'
712 #end if
713
714
715 #end if
716
717 #if str($CONDITIONAL_make_king_table.CONDITIONAL_SELECT_make_king_table) == "set":
718 --make-king-table
719
720
721 #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_0_0):
722 '${CONDITIONAL_make_king_table.make_king_table_MOD_0_0}'
723 #end if
724
725 #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_1_0):
726 '${CONDITIONAL_make_king_table.make_king_table_MOD_1_0}'
727 #end if
728
729 #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_2_0):
730 '${CONDITIONAL_make_king_table.make_king_table_MOD_2_0}'
731 #end if
732
733 #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_3_0):
734 '${CONDITIONAL_make_king_table.make_king_table_MOD_3_0}'
735 #end if
736
737 #end if
738
739 #if str($CONDITIONAL_make_rel.CONDITIONAL_SELECT_make_rel) == "set":
740 --make-rel
741
742
743 #if $str($CONDITIONAL_make_rel.make_rel_MOD_0_0):
744 '${CONDITIONAL_make_rel.make_rel_MOD_0_0}'
745 #end if
746
747 #if $str($CONDITIONAL_make_rel.make_rel_MOD_1_0):
748 '${CONDITIONAL_make_rel.make_rel_MOD_1_0}'
749 #end if
750
751 #if $str($CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_2.CONDITIONAL_SELECT_make_rel_MOD_2) == 'from_list'
752 '${CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_2.make_rel_MOD_2}'
753 #end if
754
755
756 #if $str($CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_3.CONDITIONAL_SELECT_make_rel_MOD_3) == 'from_list'
757 '${CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_3.make_rel_MOD_3}'
758 #end if
759
760
761 #end if
762
763 #if str($CONDITIONAL_make_grm_list.CONDITIONAL_SELECT_make_grm_list) == "set":
764 --make-grm-list
765
766
767 #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_0_0):
768 '${CONDITIONAL_make_grm_list.make_grm_list_MOD_0_0}'
769 #end if
770
771 #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_1_0):
772 '${CONDITIONAL_make_grm_list.make_grm_list_MOD_1_0}'
773 #end if
774
775 #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_2_0):
776 '${CONDITIONAL_make_grm_list.make_grm_list_MOD_2_0}'
777 #end if
778
779 #if $str($CONDITIONAL_make_grm_list.CONDITIONAL_make_grm_list_MOD_3.CONDITIONAL_SELECT_make_grm_list_MOD_3) == 'from_list'
780 '${CONDITIONAL_make_grm_list.CONDITIONAL_make_grm_list_MOD_3.make_grm_list_MOD_3}'
781 #end if
782
783
784 #end if
785
786 #if str($CONDITIONAL_make_grm_bin.CONDITIONAL_SELECT_make_grm_bin) == "set":
787 --make-grm-bin
788
789
790 #if $str($CONDITIONAL_make_grm_bin.make_grm_bin_MOD_0_0):
791 '${CONDITIONAL_make_grm_bin.make_grm_bin_MOD_0_0}'
792 #end if
793
794 #if $str($CONDITIONAL_make_grm_bin.make_grm_bin_MOD_1_0):
795 '${CONDITIONAL_make_grm_bin.make_grm_bin_MOD_1_0}'
796 #end if
797
798 #if $str($CONDITIONAL_make_grm_bin.CONDITIONAL_make_grm_bin_MOD_2.CONDITIONAL_SELECT_make_grm_bin_MOD_2) == 'from_list'
799 '${CONDITIONAL_make_grm_bin.CONDITIONAL_make_grm_bin_MOD_2.make_grm_bin_MOD_2}'
800 #end if
801
802
803 #end if
804
805 #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_OVERLOADED_SELECT_pca) == "form_0":
806 #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_SELECT_pca) == "set":
807 --pca
808
809 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_0_0):
810 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_0_0}'
811 #end if
812 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_1.CONDITIONAL_SELECT_pca_MOD_1) == 'from_list'
813 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_1.pca_MOD_1}'
814 #end if
815
816 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_2_0):
817 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_2_0}'
818 #end if
819 #end if
820 #end if
821
822 #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_OVERLOADED_SELECT_pca) == "form_1":
823 #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_SELECT_pca) == "set":
824 --pca
825
826 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_0.CONDITIONAL_SELECT_pca_MOD_0) == 'from_list'
827 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_0.pca_MOD_0}'
828 #end if
829
830 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_1_0):
831 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_1_0}'
832 #end if
833 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_2.CONDITIONAL_SELECT_pca_MOD_2) == 'from_list'
834 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_2.pca_MOD_2}'
835 #end if
836
837 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_3_0):
838 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_3_0}'
839 #end if
840 #end if
841 #end if
842
843 #if str($CONDITIONAL_king_cutoff.CONDITIONAL_SELECT_king_cutoff) == "set":
844 --king-cutoff
845
846
847 #if $str($CONDITIONAL_king_cutoff.king_cutoff_MOD_0_0):
848 '${CONDITIONAL_king_cutoff.king_cutoff_MOD_0_0}'
849 #end if
850
851 #if $str($CONDITIONAL_king_cutoff.king_cutoff_MOD_1_0):
852 '${CONDITIONAL_king_cutoff.king_cutoff_MOD_1_0}'
853 #end if
854
855 #end if
856
857 #if str($CONDITIONAL_write_covar.CONDITIONAL_SELECT_write_covar) == "set":
858 --write-covar
859
860
861 #if $str($CONDITIONAL_write_covar.write_covar_MOD_0_0):
862 '${CONDITIONAL_write_covar.write_covar_MOD_0_0}'
863 #end if
864
865 #end if
866
867 ${write_samples}
868
869 #if str($CONDITIONAL_write_snplist.CONDITIONAL_SELECT_write_snplist) == "set":
870 --write-snplist
871
872
873 #if $str($CONDITIONAL_write_snplist.write_snplist_MOD_0_0):
874 '${CONDITIONAL_write_snplist.write_snplist_MOD_0_0}'
875 #end if
876
877 #end if
878
879 #if str($CONDITIONAL_glm.CONDITIONAL_SELECT_glm) == "set":
880 --glm
881
882
883 #if $str($CONDITIONAL_glm.glm_MOD_0_0):
884 '${CONDITIONAL_glm.glm_MOD_0_0}'
885 #end if
886
887 #if $str($CONDITIONAL_glm.glm_MOD_1_0):
888 '${CONDITIONAL_glm.glm_MOD_1_0}'
889 #end if
890
891 #if $str($CONDITIONAL_glm.CONDITIONAL_glm_MOD_2.CONDITIONAL_SELECT_glm_MOD_2) == 'from_list'
892 '${CONDITIONAL_glm.CONDITIONAL_glm_MOD_2.glm_MOD_2}'
893 #end if
894
895
896 #if $str($CONDITIONAL_glm.glm_MOD_3_0):
897 '${CONDITIONAL_glm.glm_MOD_3_0}'
898 #end if
899
900 #if $str($CONDITIONAL_glm.glm_MOD_4_0):
901 '${CONDITIONAL_glm.glm_MOD_4_0}'
902 #end if
903
904 #end if
905
906 #if str($CONDITIONAL_score.CONDITIONAL_SELECT_score) == "set":
907 --score
908
909
910 #if $CONDITIONAL_score.score_MOD_0_0:
911 '${CONDITIONAL_score.score_MOD_0_0}'
912 #end if
913
914 #if $str($CONDITIONAL_score.score_MOD_1_0):
915 '${CONDITIONAL_score.score_MOD_1_0}'
916 #end if
917
918 #if $str($CONDITIONAL_score.score_MOD_2_0):
919 '${CONDITIONAL_score.score_MOD_2_0}'
920 #end if
921
922 #if $str($CONDITIONAL_score.score_MOD_3_0):
923 '${CONDITIONAL_score.score_MOD_3_0}'
924 #end if
925
926 #if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_4.CONDITIONAL_SELECT_score_MOD_4) == 'from_list'
927 '${CONDITIONAL_score.CONDITIONAL_score_MOD_4.score_MOD_4}'
928 #end if
929
930
931 #if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_5.CONDITIONAL_SELECT_score_MOD_5) == 'from_list'
932 '${CONDITIONAL_score.CONDITIONAL_score_MOD_5.score_MOD_5}'
933 #end if
934
935
936 #if $str($CONDITIONAL_score.score_MOD_6_0):
937 '${CONDITIONAL_score.score_MOD_6_0}'
938 #end if
939
940 #if $str($CONDITIONAL_score.score_MOD_7_0):
941 '${CONDITIONAL_score.score_MOD_7_0}'
942 #end if
943
944 #if $str($CONDITIONAL_score.score_MOD_8_0):
945 '${CONDITIONAL_score.score_MOD_8_0}'
946 #end if
947
948 #if $str($CONDITIONAL_score.score_MOD_9_0):
949 '${CONDITIONAL_score.score_MOD_9_0}'
950 #end if
951
952 #if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_10.CONDITIONAL_SELECT_score_MOD_10) == 'from_list'
953 '${CONDITIONAL_score.CONDITIONAL_score_MOD_10.score_MOD_10}'
954 #end if
955
956
957 #if $str($CONDITIONAL_score.score_MOD_11_0):
958 '${CONDITIONAL_score.score_MOD_11_0}'
959 #end if
960
961 #end if
962
963 #if str($CONDITIONAL_variant_score.CONDITIONAL_SELECT_variant_score) == "set":
964 --variant-score
965
966
967 #if $CONDITIONAL_variant_score.variant_score_MOD_0_0:
968 '${CONDITIONAL_variant_score.variant_score_MOD_0_0}'
969 #end if
970
971 #if $str($CONDITIONAL_variant_score.variant_score_MOD_1_0):
972 '${CONDITIONAL_variant_score.variant_score_MOD_1_0}'
973 #end if
974
975 #if $str($CONDITIONAL_variant_score.CONDITIONAL_variant_score_MOD_2.CONDITIONAL_SELECT_variant_score_MOD_2) == 'from_list'
976 '${CONDITIONAL_variant_score.CONDITIONAL_variant_score_MOD_2.variant_score_MOD_2}'
977 #end if
978
979
980 #end if
981
982 #if str($CONDITIONAL_adjust_file.CONDITIONAL_SELECT_adjust_file) == "set":
983 --adjust-file
984
985
986 #if $CONDITIONAL_adjust_file.adjust_file_MOD_0_0:
987 '${CONDITIONAL_adjust_file.adjust_file_MOD_0_0}'
988 #end if
989
990 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_1_0):
991 '${CONDITIONAL_adjust_file.adjust_file_MOD_1_0}'
992 #end if
993
994 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_2_0):
995 '${CONDITIONAL_adjust_file.adjust_file_MOD_2_0}'
996 #end if
997
998 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_3_0):
999 '${CONDITIONAL_adjust_file.adjust_file_MOD_3_0}'
1000 #end if
1001
1002 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_4_0):
1003 '${CONDITIONAL_adjust_file.adjust_file_MOD_4_0}'
1004 #end if
1005
1006 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_5_0):
1007 '${CONDITIONAL_adjust_file.adjust_file_MOD_5_0}'
1008 #end if
1009
1010 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_6_0):
1011 '${CONDITIONAL_adjust_file.adjust_file_MOD_6_0}'
1012 #end if
1013
1014 #end if
1015
1016 #if str($CONDITIONAL_genotyping_rate.CONDITIONAL_SELECT_genotyping_rate) == "set":
1017 --genotyping-rate
1018
1019
1020 #if $str($CONDITIONAL_genotyping_rate.genotyping_rate_MOD_0_0):
1021 '${CONDITIONAL_genotyping_rate.genotyping_rate_MOD_0_0}'
1022 #end if
1023
1024 #end if
1025
1026 ${pgen_info}
1027
1028 ${validate}
1029
1030 #if str($CONDITIONAL_zst_decompress.CONDITIONAL_SELECT_zst_decompress) == "set":
1031 --zst-decompress
1032
1033
1034 #if $str($CONDITIONAL_zst_decompress.zst_decompress_MOD_0_0):
1035 '${CONDITIONAL_zst_decompress.zst_decompress_MOD_0_0}'
1036 #end if
1037
1038 #if $str($CONDITIONAL_zst_decompress.zst_decompress_MOD_1_0):
1039 '${CONDITIONAL_zst_decompress.zst_decompress_MOD_1_0}'
1040 #end if
1041
1042 #end if
1043
1044 #if str($CONDITIONAL_silent.CONDITIONAL_SELECT_silent) == "set":
1045 --silent
1046
1047
1048 #end if
1049
1050 #if str($CONDITIONAL_double_id.CONDITIONAL_SELECT_double_id) == "set":
1051 --double-id
1052
1053
1054 #end if
1055
1056 #if str($CONDITIONAL_const_fid.CONDITIONAL_SELECT_const_fid) == "set":
1057 --const-fid
1058
1059
1060 #if $str($CONDITIONAL_const_fid.const_fid_MOD_0_0):
1061 '${CONDITIONAL_const_fid.const_fid_MOD_0_0}'
1062 #end if
1063
1064 #end if
1065
1066 #if str($CONDITIONAL_id_delim.CONDITIONAL_SELECT_id_delim) == "set":
1067 --id-delim
1068
1069
1070 #if $str($CONDITIONAL_id_delim.id_delim_MOD_0_0):
1071 '${CONDITIONAL_id_delim.id_delim_MOD_0_0}'
1072 #end if
1073
1074 #end if
1075
1076 #if str($CONDITIONAL_idspace_to.CONDITIONAL_SELECT_idspace_to) == "set":
1077 --idspace-to
1078
1079
1080 #if $str($CONDITIONAL_idspace_to.idspace_to_MOD_0_0):
1081 '${CONDITIONAL_idspace_to.idspace_to_MOD_0_0}'
1082 #end if
1083
1084 #end if
1085
1086 #if str($CONDITIONAL_iid_sid.CONDITIONAL_SELECT_iid_sid) == "set":
1087 --iid-sid
1088
1089
1090 #end if
1091
1092 #if str($CONDITIONAL_vcf_require_gt.CONDITIONAL_SELECT_vcf_require_gt) == "set":
1093 --vcf-require-gt
1094
1095
1096 #end if
1097
1098 #if str($CONDITIONAL_vcf_min_gq.CONDITIONAL_SELECT_vcf_min_gq) == "set":
1099 --vcf-min-gq
1100
1101
1102 #if $str($CONDITIONAL_vcf_min_gq.vcf_min_gq_MOD_0_0):
1103 '${CONDITIONAL_vcf_min_gq.vcf_min_gq_MOD_0_0}'
1104 #end if
1105
1106 #end if
1107
1108 #if str($CONDITIONAL_vcf_max_dp.CONDITIONAL_SELECT_vcf_max_dp) == "set":
1109 --vcf-max-dp
1110
1111
1112 #if $str($CONDITIONAL_vcf_max_dp.vcf_max_dp_MOD_0_0):
1113 '${CONDITIONAL_vcf_max_dp.vcf_max_dp_MOD_0_0}'
1114 #end if
1115
1116 #end if
1117
1118 #if str($CONDITIONAL_vcf_min_dp.CONDITIONAL_SELECT_vcf_min_dp) == "set":
1119 --vcf-min-dp
1120
1121
1122 #if $str($CONDITIONAL_vcf_min_dp.vcf_min_dp_MOD_0_0):
1123 '${CONDITIONAL_vcf_min_dp.vcf_min_dp_MOD_0_0}'
1124 #end if
1125
1126 #end if
1127
1128 #if str($CONDITIONAL_vcf_half_call.CONDITIONAL_SELECT_vcf_half_call) == "set":
1129 --vcf-half-call
1130
1131
1132 #if $str($CONDITIONAL_vcf_half_call.vcf_half_call_MOD_0_0):
1133 '${CONDITIONAL_vcf_half_call.vcf_half_call_MOD_0_0}'
1134 #end if
1135
1136 #end if
1137
1138 #if str($CONDITIONAL_oxford_single_chr.CONDITIONAL_SELECT_oxford_single_chr) == "set":
1139 --oxford-single-chr
1140
1141
1142 #if $str($CONDITIONAL_oxford_single_chr.oxford_single_chr_MOD_0_0):
1143 '${CONDITIONAL_oxford_single_chr.oxford_single_chr_MOD_0_0}'
1144 #end if
1145
1146 #end if
1147
1148 #if str($CONDITIONAL_missing_code.CONDITIONAL_SELECT_missing_code) == "set":
1149 --missing-code
1150
1151
1152 #if $str($CONDITIONAL_missing_code.missing_code_MOD_0_0):
1153 '${CONDITIONAL_missing_code.missing_code_MOD_0_0}'
1154 #end if
1155
1156 #end if
1157
1158 #if str($CONDITIONAL_hard_call_threshold.CONDITIONAL_SELECT_hard_call_threshold) == "set":
1159 --hard-call-threshold
1160
1161
1162 #if $str($CONDITIONAL_hard_call_threshold.hard_call_threshold_MOD_0_0):
1163 '${CONDITIONAL_hard_call_threshold.hard_call_threshold_MOD_0_0}'
1164 #end if
1165
1166 #end if
1167
1168 #if str($CONDITIONAL_dosage_erase_threshold.CONDITIONAL_SELECT_dosage_erase_threshold) == "set":
1169 --dosage-erase-threshold
1170
1171
1172 #if $str($CONDITIONAL_dosage_erase_threshold.dosage_erase_threshold_MOD_0_0):
1173 '${CONDITIONAL_dosage_erase_threshold.dosage_erase_threshold_MOD_0_0}'
1174 #end if
1175
1176 #end if
1177
1178 #if str($CONDITIONAL_import_dosage_certainty.CONDITIONAL_SELECT_import_dosage_certainty) == "set":
1179 --import-dosage-certainty
1180
1181
1182 #if $str($CONDITIONAL_import_dosage_certainty.import_dosage_certainty_MOD_0_0):
1183 '${CONDITIONAL_import_dosage_certainty.import_dosage_certainty_MOD_0_0}'
1184 #end if
1185
1186 #end if
1187
1188 #if str($CONDITIONAL_input_missing_genotype.CONDITIONAL_SELECT_input_missing_genotype) == "set":
1189 --input-missing-genotype
1190
1191
1192 #if $str($CONDITIONAL_input_missing_genotype.input_missing_genotype_MOD_0_0):
1193 '${CONDITIONAL_input_missing_genotype.input_missing_genotype_MOD_0_0}'
1194 #end if
1195
1196 #end if
1197
1198 #if str($CONDITIONAL_allow_extra_chr.CONDITIONAL_SELECT_allow_extra_chr) == "set":
1199 --allow-extra-chr
1200
1201
1202 #end if
1203
1204 #if str($CONDITIONAL_chr_set.CONDITIONAL_SELECT_chr_set) == "set":
1205 --chr-set
1206
1207
1208 #if $str($CONDITIONAL_chr_set.chr_set_MOD_0_0):
1209 '${CONDITIONAL_chr_set.chr_set_MOD_0_0}'
1210 #end if
1211
1212 #if $str($CONDITIONAL_chr_set.chr_set_MOD_1_0):
1213 '${CONDITIONAL_chr_set.chr_set_MOD_1_0}'
1214 #end if
1215
1216 #if $str($CONDITIONAL_chr_set.chr_set_MOD_2_0):
1217 '${CONDITIONAL_chr_set.chr_set_MOD_2_0}'
1218 #end if
1219
1220 #if $str($CONDITIONAL_chr_set.chr_set_MOD_3_0):
1221 '${CONDITIONAL_chr_set.chr_set_MOD_3_0}'
1222 #end if
1223
1224 #if $str($CONDITIONAL_chr_set.chr_set_MOD_4_0):
1225 '${CONDITIONAL_chr_set.chr_set_MOD_4_0}'
1226 #end if
1227
1228 #end if
1229
1230 #if str($CONDITIONAL_cow.CONDITIONAL_SELECT_cow) == "set":
1231 --cow
1232
1233
1234 #end if
1235
1236 #if str($CONDITIONAL_dog.CONDITIONAL_SELECT_dog) == "set":
1237 --dog
1238
1239
1240 #end if
1241
1242 #if str($CONDITIONAL_horse.CONDITIONAL_SELECT_horse) == "set":
1243 --horse
1244
1245
1246 #end if
1247
1248 #if str($CONDITIONAL_mouse.CONDITIONAL_SELECT_mouse) == "set":
1249 --mouse
1250
1251
1252 #end if
1253
1254 #if str($CONDITIONAL_rice.CONDITIONAL_SELECT_rice) == "set":
1255 --rice
1256
1257
1258 #end if
1259
1260 #if str($CONDITIONAL_sheep.CONDITIONAL_SELECT_sheep) == "set":
1261 --sheep
1262
1263
1264 #end if
1265
1266 #if str($CONDITIONAL_autosome_num.CONDITIONAL_SELECT_autosome_num) == "set":
1267 --autosome-num
1268
1269
1270 #if $str($CONDITIONAL_autosome_num.autosome_num_MOD_0_0):
1271 '${CONDITIONAL_autosome_num.autosome_num_MOD_0_0}'
1272 #end if
1273
1274 #end if
1275
1276 #if str($CONDITIONAL_human.CONDITIONAL_SELECT_human) == "set":
1277 --human
1278
1279
1280 #end if
1281
1282 #if str($CONDITIONAL_chr_override.CONDITIONAL_SELECT_chr_override) == "set":
1283 --chr-override
1284
1285
1286 #if $str($CONDITIONAL_chr_override.chr_override_MOD_0_0):
1287 '${CONDITIONAL_chr_override.chr_override_MOD_0_0}'
1288 #end if
1289
1290 #end if
1291
1292 #if str($CONDITIONAL_var_min_qual.CONDITIONAL_SELECT_var_min_qual) == "set":
1293 --var-min-qual
1294
1295
1296 #if $str($CONDITIONAL_var_min_qual.var_min_qual_MOD_0_0):
1297 '${CONDITIONAL_var_min_qual.var_min_qual_MOD_0_0}'
1298 #end if
1299
1300 #end if
1301
1302 #if str($CONDITIONAL_var_filter.CONDITIONAL_SELECT_var_filter) == "set":
1303 --var-filter
1304
1305
1306 #if $str($CONDITIONAL_var_filter.var_filter_MOD_0_0):
1307 '${CONDITIONAL_var_filter.var_filter_MOD_0_0}'
1308 #end if
1309
1310 #end if
1311
1312 #if str($CONDITIONAL_extract_if_info.CONDITIONAL_SELECT_extract_if_info) == "set":
1313 --extract-if-info
1314
1315
1316 #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_0_0):
1317 '${CONDITIONAL_extract_if_info.extract_if_info_MOD_0_0}'
1318 #end if
1319
1320 #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_1_0):
1321 '${CONDITIONAL_extract_if_info.extract_if_info_MOD_1_0}'
1322 #end if
1323
1324 #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_2_0):
1325 '${CONDITIONAL_extract_if_info.extract_if_info_MOD_2_0}'
1326 #end if
1327
1328 #end if
1329
1330 #if str($CONDITIONAL_exclude_if_info.CONDITIONAL_SELECT_exclude_if_info) == "set":
1331 --exclude-if-info
1332
1333
1334 #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_0_0):
1335 '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_0_0}'
1336 #end if
1337
1338 #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_1_0):
1339 '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_1_0}'
1340 #end if
1341
1342 #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_2_0):
1343 '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_2_0}'
1344 #end if
1345
1346 #end if
1347
1348 #if str($CONDITIONAL_require_info.CONDITIONAL_SELECT_require_info) == "set":
1349 --require-info
1350
1351
1352 #if $str($CONDITIONAL_require_info.require_info_MOD_0_0):
1353 '${CONDITIONAL_require_info.require_info_MOD_0_0}'
1354 #end if
1355
1356 #end if
1357
1358 #if str($CONDITIONAL_require_no_info.CONDITIONAL_SELECT_require_no_info) == "set":
1359 --require-no-info
1360
1361
1362 #if $str($CONDITIONAL_require_no_info.require_no_info_MOD_0_0):
1363 '${CONDITIONAL_require_no_info.require_no_info_MOD_0_0}'
1364 #end if
1365
1366 #if $str($CONDITIONAL_require_no_info.require_no_info_MOD_1_0):
1367 '${CONDITIONAL_require_no_info.require_no_info_MOD_1_0}'
1368 #end if
1369
1370 #end if
1371
1372 #if str($CONDITIONAL_extract_col_cond.CONDITIONAL_SELECT_extract_col_cond) == "set":
1373 --extract-col-cond
1374
1375
1376 #if $CONDITIONAL_extract_col_cond.extract_col_cond_MOD_0_0:
1377 '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_0_0}'
1378 #end if
1379
1380 #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_1_0):
1381 '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_1_0}'
1382 #end if
1383
1384 #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_2_0):
1385 '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_2_0}'
1386 #end if
1387
1388 #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_3_0):
1389 '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_3_0}'
1390 #end if
1391
1392 #end if
1393
1394 #if str($CONDITIONAL_extract_col_cond_match.CONDITIONAL_SELECT_extract_col_cond_match) == "set":
1395 --extract-col-cond-match
1396
1397
1398 #if $str($CONDITIONAL_extract_col_cond_match.extract_col_cond_match_MOD_0_0):
1399 '${CONDITIONAL_extract_col_cond_match.extract_col_cond_match_MOD_0_0}'
1400 #end if
1401
1402 #end if
1403
1404 #if str($CONDITIONAL_extract_col_cond_mismatch.CONDITIONAL_SELECT_extract_col_cond_mismatch) == "set":
1405 --extract-col-cond-mismatch
1406
1407
1408 #if $str($CONDITIONAL_extract_col_cond_mismatch.extract_col_cond_mismatch_MOD_0_0):
1409 '${CONDITIONAL_extract_col_cond_mismatch.extract_col_cond_mismatch_MOD_0_0}'
1410 #end if
1411
1412 #end if
1413
1414 ${extract_col_cond_substr}
1415
1416 #if str($CONDITIONAL_extract_col_cond_min.CONDITIONAL_SELECT_extract_col_cond_min) == "set":
1417 --extract-col-cond-min
1418
1419
1420 #if $str($CONDITIONAL_extract_col_cond_min.extract_col_cond_min_MOD_0_0):
1421 '${CONDITIONAL_extract_col_cond_min.extract_col_cond_min_MOD_0_0}'
1422 #end if
1423
1424 #end if
1425
1426 #if str($CONDITIONAL_extract_col_cond_max.CONDITIONAL_SELECT_extract_col_cond_max) == "set":
1427 --extract-col-cond-max
1428
1429
1430 #if $str($CONDITIONAL_extract_col_cond_max.extract_col_cond_max_MOD_0_0):
1431 '${CONDITIONAL_extract_col_cond_max.extract_col_cond_max_MOD_0_0}'
1432 #end if
1433
1434 #end if
1435
1436 #if str($CONDITIONAL_pheno.CONDITIONAL_SELECT_pheno) == "set":
1437 --pheno
1438
1439
1440 #if $str($CONDITIONAL_pheno.pheno_MOD_0_0):
1441 '${CONDITIONAL_pheno.pheno_MOD_0_0}'
1442 #end if
1443
1444 #if $CONDITIONAL_pheno.pheno_MOD_1_0:
1445 '${CONDITIONAL_pheno.pheno_MOD_1_0}'
1446 #end if
1447
1448 #end if
1449
1450 #if str($CONDITIONAL_pheno_name.CONDITIONAL_SELECT_pheno_name) == "set":
1451 --pheno-name
1452
1453
1454 #if $str($CONDITIONAL_pheno_name.pheno_name_MOD_0_0):
1455 '${CONDITIONAL_pheno_name.pheno_name_MOD_0_0}'
1456 #end if
1457
1458 #end if
1459
1460 #if str($CONDITIONAL_pheno_col_nums.CONDITIONAL_SELECT_pheno_col_nums) == "set":
1461 --pheno-col-nums
1462
1463
1464 #if $str($CONDITIONAL_pheno_col_nums.pheno_col_nums_MOD_0_0):
1465 '${CONDITIONAL_pheno_col_nums.pheno_col_nums_MOD_0_0}'
1466 #end if
1467
1468 #end if
1469
1470 #if str($CONDITIONAL_no_psam_pheno.CONDITIONAL_SELECT_no_psam_pheno) == "set":
1471 --no-psam-pheno
1472
1473
1474 #end if
1475
1476 #if str($CONDITIONAL_strict_sid0.CONDITIONAL_SELECT_strict_sid0) == "set":
1477 --strict-sid0
1478
1479
1480 #end if
1481
1482 #if str($CONDITIONAL_input_missing_phenotype.CONDITIONAL_SELECT_input_missing_phenotype) == "set":
1483 --input-missing-phenotype
1484
1485
1486 #if $str($CONDITIONAL_input_missing_phenotype.input_missing_phenotype_MOD_0_0):
1487 '${CONDITIONAL_input_missing_phenotype.input_missing_phenotype_MOD_0_0}'
1488 #end if
1489
1490 #end if
1491
1492 #if str($CONDITIONAL_no_input_missing_phenotype.CONDITIONAL_SELECT_no_input_missing_phenotype) == "set":
1493 --no-input-missing-phenotype
1494
1495
1496 #end if
1497
1498 #if str($CONDITIONAL_GALAXY_1.CONDITIONAL_SELECT_GALAXY_1) == "set":
1499 --1
1500
1501
1502 #end if
1503
1504 #if str($CONDITIONAL_missing_catname.CONDITIONAL_SELECT_missing_catname) == "set":
1505 --missing-catname
1506
1507
1508 #if $str($CONDITIONAL_missing_catname.missing_catname_MOD_0_0):
1509 '${CONDITIONAL_missing_catname.missing_catname_MOD_0_0}'
1510 #end if
1511
1512 #end if
1513
1514 #if str($CONDITIONAL_covar.CONDITIONAL_SELECT_covar) == "set":
1515 --covar
1516
1517
1518 #if $str($CONDITIONAL_covar.covar_MOD_0_0):
1519 '${CONDITIONAL_covar.covar_MOD_0_0}'
1520 #end if
1521
1522 #if $CONDITIONAL_covar.covar_MOD_1_0:
1523 '${CONDITIONAL_covar.covar_MOD_1_0}'
1524 #end if
1525
1526 #end if
1527
1528 #if str($CONDITIONAL_covar_name.CONDITIONAL_SELECT_covar_name) == "set":
1529 --covar-name
1530
1531
1532 #if $str($CONDITIONAL_covar_name.covar_name_MOD_0_0):
1533 '${CONDITIONAL_covar_name.covar_name_MOD_0_0}'
1534 #end if
1535
1536 #end if
1537
1538 #if str($CONDITIONAL_covar_col_nums.CONDITIONAL_SELECT_covar_col_nums) == "set":
1539 --covar-col-nums
1540
1541
1542 #if $str($CONDITIONAL_covar_col_nums.covar_col_nums_MOD_0_0):
1543 '${CONDITIONAL_covar_col_nums.covar_col_nums_MOD_0_0}'
1544 #end if
1545
1546 #end if
1547
1548 #if str($CONDITIONAL_within.CONDITIONAL_SELECT_within) == "set":
1549 --within
1550
1551
1552 #if $CONDITIONAL_within.within_MOD_0_0:
1553 '${CONDITIONAL_within.within_MOD_0_0}'
1554 #end if
1555
1556 #if $str($CONDITIONAL_within.within_MOD_1_0):
1557 '${CONDITIONAL_within.within_MOD_1_0}'
1558 #end if
1559
1560 #end if
1561
1562 #if str($CONDITIONAL_mwithin.CONDITIONAL_SELECT_mwithin) == "set":
1563 --mwithin
1564
1565
1566 #if $str($CONDITIONAL_mwithin.mwithin_MOD_0_0):
1567 '${CONDITIONAL_mwithin.mwithin_MOD_0_0}'
1568 #end if
1569
1570 #end if
1571
1572 #if str($CONDITIONAL_family.CONDITIONAL_SELECT_family) == "set":
1573 --family
1574
1575
1576 #if $str($CONDITIONAL_family.family_MOD_0_0):
1577 '${CONDITIONAL_family.family_MOD_0_0}'
1578 #end if
1579
1580 #end if
1581
1582 #if str($CONDITIONAL_family_missing_catname.CONDITIONAL_SELECT_family_missing_catname) == "set":
1583 --family-missing-catname
1584
1585
1586 #if $str($CONDITIONAL_family_missing_catname.family_missing_catname_MOD_0_0):
1587 '${CONDITIONAL_family_missing_catname.family_missing_catname_MOD_0_0}'
1588 #end if
1589
1590 #end if
1591
1592 #if str($CONDITIONAL_keep.CONDITIONAL_SELECT_keep) == "set":
1593 --keep
1594
1595
1596 #if $str($CONDITIONAL_keep.keep_MOD_0_0):
1597 '${CONDITIONAL_keep.keep_MOD_0_0}'
1598 #end if
1599
1600 #end if
1601
1602 #if str($CONDITIONAL_remove.CONDITIONAL_SELECT_remove) == "set":
1603 --remove
1604
1605
1606 #if $str($CONDITIONAL_remove.remove_MOD_0_0):
1607 '${CONDITIONAL_remove.remove_MOD_0_0}'
1608 #end if
1609
1610 #end if
1611
1612 #if str($CONDITIONAL_keep_fam.CONDITIONAL_SELECT_keep_fam) == "set":
1613 --keep-fam
1614
1615
1616 #if $str($CONDITIONAL_keep_fam.keep_fam_MOD_0_0):
1617 '${CONDITIONAL_keep_fam.keep_fam_MOD_0_0}'
1618 #end if
1619
1620 #end if
1621
1622 #if str($CONDITIONAL_remove_fam.CONDITIONAL_SELECT_remove_fam) == "set":
1623 --remove-fam
1624
1625
1626 #if $str($CONDITIONAL_remove_fam.remove_fam_MOD_0_0):
1627 '${CONDITIONAL_remove_fam.remove_fam_MOD_0_0}'
1628 #end if
1629
1630 #end if
1631
1632 #if str($CONDITIONAL_extract.CONDITIONAL_SELECT_extract) == "set":
1633 --extract
1634
1635
1636 #if $str($CONDITIONAL_extract.CONDITIONAL_extract_MOD_0.CONDITIONAL_SELECT_extract_MOD_0) == 'from_list'
1637 '${CONDITIONAL_extract.CONDITIONAL_extract_MOD_0.extract_MOD_0}'
1638 #end if
1639
1640
1641 #if $str($CONDITIONAL_extract.extract_MOD_1_0):
1642 '${CONDITIONAL_extract.extract_MOD_1_0}'
1643 #end if
1644
1645 #end if
1646
1647 #if str($CONDITIONAL_exclude.CONDITIONAL_SELECT_exclude) == "set":
1648 --exclude
1649
1650
1651 #if $str($CONDITIONAL_exclude.CONDITIONAL_exclude_MOD_0.CONDITIONAL_SELECT_exclude_MOD_0) == 'from_list'
1652 '${CONDITIONAL_exclude.CONDITIONAL_exclude_MOD_0.exclude_MOD_0}'
1653 #end if
1654
1655
1656 #if $str($CONDITIONAL_exclude.exclude_MOD_1_0):
1657 '${CONDITIONAL_exclude.exclude_MOD_1_0}'
1658 #end if
1659
1660 #end if
1661
1662 #if str($CONDITIONAL_extract_intersect.CONDITIONAL_SELECT_extract_intersect) == "set":
1663 --extract-intersect
1664
1665
1666 #if $str($CONDITIONAL_extract_intersect.CONDITIONAL_extract_intersect_MOD_0.CONDITIONAL_SELECT_extract_intersect_MOD_0) == 'from_list'
1667 '${CONDITIONAL_extract_intersect.CONDITIONAL_extract_intersect_MOD_0.extract_intersect_MOD_0}'
1668 #end if
1669
1670
1671 #if $str($CONDITIONAL_extract_intersect.extract_intersect_MOD_1_0):
1672 '${CONDITIONAL_extract_intersect.extract_intersect_MOD_1_0}'
1673 #end if
1674
1675 #end if
1676
1677 #if str($CONDITIONAL_keep_cats.CONDITIONAL_SELECT_keep_cats) == "set":
1678 --keep-cats
1679
1680
1681 #if $CONDITIONAL_keep_cats.keep_cats_MOD_0_0:
1682 '${CONDITIONAL_keep_cats.keep_cats_MOD_0_0}'
1683 #end if
1684
1685 #end if
1686
1687 #if str($CONDITIONAL_keep_cat_names.CONDITIONAL_SELECT_keep_cat_names) == "set":
1688 --keep-cat-names
1689
1690
1691 #if $str($CONDITIONAL_keep_cat_names.keep_cat_names_MOD_0_0):
1692 '${CONDITIONAL_keep_cat_names.keep_cat_names_MOD_0_0}'
1693 #end if
1694
1695 #end if
1696
1697 #if str($CONDITIONAL_keep_cat_pheno.CONDITIONAL_SELECT_keep_cat_pheno) == "set":
1698 --keep-cat-pheno
1699
1700
1701 #if $str($CONDITIONAL_keep_cat_pheno.keep_cat_pheno_MOD_0_0):
1702 '${CONDITIONAL_keep_cat_pheno.keep_cat_pheno_MOD_0_0}'
1703 #end if
1704
1705 #end if
1706
1707 #if str($CONDITIONAL_remove_cats.CONDITIONAL_SELECT_remove_cats) == "set":
1708 --remove-cats
1709
1710
1711 #if $CONDITIONAL_remove_cats.remove_cats_MOD_0_0:
1712 '${CONDITIONAL_remove_cats.remove_cats_MOD_0_0}'
1713 #end if
1714
1715 #end if
1716
1717 #if str($CONDITIONAL_remove_cat_names.CONDITIONAL_SELECT_remove_cat_names) == "set":
1718 --remove-cat-names
1719
1720
1721 #if $str($CONDITIONAL_remove_cat_names.remove_cat_names_MOD_0_0):
1722 '${CONDITIONAL_remove_cat_names.remove_cat_names_MOD_0_0}'
1723 #end if
1724
1725 #end if
1726
1727 #if str($CONDITIONAL_remove_cat_pheno.CONDITIONAL_SELECT_remove_cat_pheno) == "set":
1728 --remove-cat-pheno
1729
1730
1731 #if $str($CONDITIONAL_remove_cat_pheno.remove_cat_pheno_MOD_0_0):
1732 '${CONDITIONAL_remove_cat_pheno.remove_cat_pheno_MOD_0_0}'
1733 #end if
1734
1735 #end if
1736
1737 #if str($CONDITIONAL_split_cat_pheno.CONDITIONAL_SELECT_split_cat_pheno) == "set":
1738 --split-cat-pheno
1739
1740
1741 #if $str($CONDITIONAL_split_cat_pheno.CONDITIONAL_split_cat_pheno_MOD_0.CONDITIONAL_SELECT_split_cat_pheno_MOD_0) == 'from_list'
1742 '${CONDITIONAL_split_cat_pheno.CONDITIONAL_split_cat_pheno_MOD_0.split_cat_pheno_MOD_0}'
1743 #end if
1744
1745
1746 #if $str($CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_1_0):
1747 '${CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_1_0}'
1748 #end if
1749
1750 #if $str($CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_2_0):
1751 '${CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_2_0}'
1752 #end if
1753
1754 #end if
1755
1756 #if str($CONDITIONAL_loop_cats.CONDITIONAL_SELECT_loop_cats) == "set":
1757 --loop-cats
1758
1759
1760 #if $str($CONDITIONAL_loop_cats.loop_cats_MOD_0_0):
1761 '${CONDITIONAL_loop_cats.loop_cats_MOD_0_0}'
1762 #end if
1763
1764 #end if
1765
1766 #if str($CONDITIONAL_no_id_header.CONDITIONAL_SELECT_no_id_header) == "set":
1767 --no-id-header
1768
1769
1770 #if $str($CONDITIONAL_no_id_header.no_id_header_MOD_0_0):
1771 '${CONDITIONAL_no_id_header.no_id_header_MOD_0_0}'
1772 #end if
1773
1774 #end if
1775
1776 #if str($CONDITIONAL_variance_standardize.CONDITIONAL_SELECT_variance_standardize) == "set":
1777 --variance-standardize
1778
1779
1780 #if $str($CONDITIONAL_variance_standardize.variance_standardize_MOD_0_0):
1781 '${CONDITIONAL_variance_standardize.variance_standardize_MOD_0_0}'
1782 #end if
1783
1784 #end if
1785
1786 #if str($CONDITIONAL_covar_variance_standardize.CONDITIONAL_SELECT_covar_variance_standardize) == "set":
1787 --covar-variance-standardize
1788
1789
1790 #if $str($CONDITIONAL_covar_variance_standardize.covar_variance_standardize_MOD_0_0):
1791 '${CONDITIONAL_covar_variance_standardize.covar_variance_standardize_MOD_0_0}'
1792 #end if
1793
1794 #end if
1795
1796 #if str($CONDITIONAL_quantile_normalize.CONDITIONAL_SELECT_quantile_normalize) == "set":
1797 --quantile-normalize
1798
1799
1800 #if $str($CONDITIONAL_quantile_normalize.quantile_normalize_MOD_0_0):
1801 '${CONDITIONAL_quantile_normalize.quantile_normalize_MOD_0_0}'
1802 #end if
1803
1804 #end if
1805
1806 #if str($CONDITIONAL_pheno_quantile_normalize.CONDITIONAL_SELECT_pheno_quantile_normalize) == "set":
1807 --pheno-quantile-normalize
1808
1809
1810 #if $str($CONDITIONAL_pheno_quantile_normalize.pheno_quantile_normalize_MOD_0_0):
1811 '${CONDITIONAL_pheno_quantile_normalize.pheno_quantile_normalize_MOD_0_0}'
1812 #end if
1813
1814 #end if
1815
1816 #if str($CONDITIONAL_covar_quantile_normalize.CONDITIONAL_SELECT_covar_quantile_normalize) == "set":
1817 --covar-quantile-normalize
1818
1819
1820 #if $str($CONDITIONAL_covar_quantile_normalize.covar_quantile_normalize_MOD_0_0):
1821 '${CONDITIONAL_covar_quantile_normalize.covar_quantile_normalize_MOD_0_0}'
1822 #end if
1823
1824 #end if
1825
1826 #if str($CONDITIONAL_chr.CONDITIONAL_SELECT_chr) == "set":
1827 --chr
1828
1829
1830 #if $str($CONDITIONAL_chr.chr_MOD_0_0):
1831 '${CONDITIONAL_chr.chr_MOD_0_0}'
1832 #end if
1833
1834 #end if
1835
1836 #if str($CONDITIONAL_not_chr.CONDITIONAL_SELECT_not_chr) == "set":
1837 --not-chr
1838
1839
1840 #if $str($CONDITIONAL_not_chr.not_chr_MOD_0_0):
1841 '${CONDITIONAL_not_chr.not_chr_MOD_0_0}'
1842 #end if
1843
1844 #end if
1845
1846 #if str($CONDITIONAL_autosome.CONDITIONAL_SELECT_autosome) == "set":
1847 --autosome
1848
1849
1850 #end if
1851
1852 #if str($CONDITIONAL_autosome_par.CONDITIONAL_SELECT_autosome_par) == "set":
1853 --autosome-par
1854
1855
1856 #end if
1857
1858 #if str($CONDITIONAL_snps_only.CONDITIONAL_SELECT_snps_only) == "set":
1859 --snps-only
1860
1861
1862 #if $str($CONDITIONAL_snps_only.snps_only_MOD_0_0):
1863 '${CONDITIONAL_snps_only.snps_only_MOD_0_0}'
1864 #end if
1865
1866 #end if
1867
1868 #if str($CONDITIONAL_from.CONDITIONAL_SELECT_from) == "set":
1869 --from
1870
1871
1872 #if $str($CONDITIONAL_from.from_MOD_0_0):
1873 '${CONDITIONAL_from.from_MOD_0_0}'
1874 #end if
1875
1876 #end if
1877
1878 #if str($CONDITIONAL_to.CONDITIONAL_SELECT_to) == "set":
1879 --to
1880
1881
1882 #if $str($CONDITIONAL_to.to_MOD_0_0):
1883 '${CONDITIONAL_to.to_MOD_0_0}'
1884 #end if
1885
1886 #end if
1887
1888 #if str($CONDITIONAL_snp.CONDITIONAL_SELECT_snp) == "set":
1889 --snp
1890
1891
1892 #if $str($CONDITIONAL_snp.snp_MOD_0_0):
1893 '${CONDITIONAL_snp.snp_MOD_0_0}'
1894 #end if
1895
1896 #end if
1897
1898 #if str($CONDITIONAL_exclude_snp.CONDITIONAL_SELECT_exclude_snp) == "set":
1899 --exclude-snp
1900
1901
1902 #if $str($CONDITIONAL_exclude_snp.exclude_snp_MOD_0_0):
1903 '${CONDITIONAL_exclude_snp.exclude_snp_MOD_0_0}'
1904 #end if
1905
1906 #end if
1907
1908 #if str($CONDITIONAL_window.CONDITIONAL_SELECT_window) == "set":
1909 --window
1910
1911
1912 #if $str($CONDITIONAL_window.window_MOD_0_0):
1913 '${CONDITIONAL_window.window_MOD_0_0}'
1914 #end if
1915
1916 #end if
1917
1918 #if str($CONDITIONAL_from_bp.CONDITIONAL_SELECT_from_bp) == "set":
1919 --from-bp
1920
1921
1922 #if $str($CONDITIONAL_from_bp.from_bp_MOD_0_0):
1923 '${CONDITIONAL_from_bp.from_bp_MOD_0_0}'
1924 #end if
1925
1926 #end if
1927
1928 #if str($CONDITIONAL_to_bp.CONDITIONAL_SELECT_to_bp) == "set":
1929 --to-bp
1930
1931
1932 #if $str($CONDITIONAL_to_bp.to_bp_MOD_0_0):
1933 '${CONDITIONAL_to_bp.to_bp_MOD_0_0}'
1934 #end if
1935
1936 #end if
1937
1938 #if str($CONDITIONAL_from_kb.CONDITIONAL_SELECT_from_kb) == "set":
1939 --from-kb
1940
1941
1942 #if $str($CONDITIONAL_from_kb.from_kb_MOD_0_0):
1943 '${CONDITIONAL_from_kb.from_kb_MOD_0_0}'
1944 #end if
1945
1946 #end if
1947
1948 #if str($CONDITIONAL_to_kb.CONDITIONAL_SELECT_to_kb) == "set":
1949 --to-kb
1950
1951
1952 #if $str($CONDITIONAL_to_kb.to_kb_MOD_0_0):
1953 '${CONDITIONAL_to_kb.to_kb_MOD_0_0}'
1954 #end if
1955
1956 #end if
1957
1958 #if str($CONDITIONAL_from_mb.CONDITIONAL_SELECT_from_mb) == "set":
1959 --from-mb
1960
1961
1962 #if $str($CONDITIONAL_from_mb.from_mb_MOD_0_0):
1963 '${CONDITIONAL_from_mb.from_mb_MOD_0_0}'
1964 #end if
1965
1966 #end if
1967
1968 #if str($CONDITIONAL_to_mb.CONDITIONAL_SELECT_to_mb) == "set":
1969 --to-mb
1970
1971
1972 #if $str($CONDITIONAL_to_mb.to_mb_MOD_0_0):
1973 '${CONDITIONAL_to_mb.to_mb_MOD_0_0}'
1974 #end if
1975
1976 #end if
1977
1978 #if str($CONDITIONAL_snps.CONDITIONAL_SELECT_snps) == "set":
1979 --snps
1980
1981
1982 #if $str($CONDITIONAL_snps.snps_MOD_0_0):
1983 '${CONDITIONAL_snps.snps_MOD_0_0}'
1984 #end if
1985
1986 #end if
1987
1988 #if str($CONDITIONAL_exclude_snps.CONDITIONAL_SELECT_exclude_snps) == "set":
1989 --exclude-snps
1990
1991
1992 #if $str($CONDITIONAL_exclude_snps.exclude_snps_MOD_0_0):
1993 '${CONDITIONAL_exclude_snps.exclude_snps_MOD_0_0}'
1994 #end if
1995
1996 #end if
1997
1998 #if str($CONDITIONAL_force_intersect.CONDITIONAL_SELECT_force_intersect) == "set":
1999 --force-intersect
2000
2001
2002 #end if
2003
2004 #if str($CONDITIONAL_thin.CONDITIONAL_SELECT_thin) == "set":
2005 --thin
2006
2007
2008 #if $str($CONDITIONAL_thin.thin_MOD_0_0):
2009 '${CONDITIONAL_thin.thin_MOD_0_0}'
2010 #end if
2011
2012 #end if
2013
2014 #if str($CONDITIONAL_thin_count.CONDITIONAL_SELECT_thin_count) == "set":
2015 --thin-count
2016
2017
2018 #if $str($CONDITIONAL_thin_count.thin_count_MOD_0_0):
2019 '${CONDITIONAL_thin_count.thin_count_MOD_0_0}'
2020 #end if
2021
2022 #end if
2023
2024 #if str($CONDITIONAL_bp_space.CONDITIONAL_SELECT_bp_space) == "set":
2025 --bp-space
2026
2027
2028 #if $str($CONDITIONAL_bp_space.bp_space_MOD_0_0):
2029 '${CONDITIONAL_bp_space.bp_space_MOD_0_0}'
2030 #end if
2031
2032 #end if
2033
2034 #if str($CONDITIONAL_thin_indiv.CONDITIONAL_SELECT_thin_indiv) == "set":
2035 --thin-indiv
2036
2037
2038 #if $str($CONDITIONAL_thin_indiv.thin_indiv_MOD_0_0):
2039 '${CONDITIONAL_thin_indiv.thin_indiv_MOD_0_0}'
2040 #end if
2041
2042 #end if
2043
2044 #if str($CONDITIONAL_thin_indiv_count.CONDITIONAL_SELECT_thin_indiv_count) == "set":
2045 --thin-indiv-count
2046
2047
2048 #if $str($CONDITIONAL_thin_indiv_count.thin_indiv_count_MOD_0_0):
2049 '${CONDITIONAL_thin_indiv_count.thin_indiv_count_MOD_0_0}'
2050 #end if
2051
2052 #end if
2053
2054 #if str($CONDITIONAL_keep_col_match.CONDITIONAL_SELECT_keep_col_match) == "set":
2055 --keep-col-match
2056
2057
2058 #if $CONDITIONAL_keep_col_match.keep_col_match_MOD_0_0:
2059 '${CONDITIONAL_keep_col_match.keep_col_match_MOD_0_0}'
2060 #end if
2061
2062 #if $str($CONDITIONAL_keep_col_match.keep_col_match_MOD_1_0):
2063 '${CONDITIONAL_keep_col_match.keep_col_match_MOD_1_0}'
2064 #end if
2065
2066 #end if
2067
2068 #if str($CONDITIONAL_keep_col_match_name.CONDITIONAL_SELECT_keep_col_match_name) == "set":
2069 --keep-col-match-name
2070
2071
2072 #if $str($CONDITIONAL_keep_col_match_name.keep_col_match_name_MOD_0_0):
2073 '${CONDITIONAL_keep_col_match_name.keep_col_match_name_MOD_0_0}'
2074 #end if
2075
2076 #end if
2077
2078 #if str($CONDITIONAL_keep_col_match_num.CONDITIONAL_SELECT_keep_col_match_num) == "set":
2079 --keep-col-match-num
2080
2081
2082 #if $str($CONDITIONAL_keep_col_match_num.keep_col_match_num_MOD_0_0):
2083 '${CONDITIONAL_keep_col_match_num.keep_col_match_num_MOD_0_0}'
2084 #end if
2085
2086 #end if
2087
2088 #if str($CONDITIONAL_geno.CONDITIONAL_SELECT_geno) == "set":
2089 --geno
2090
2091
2092 #if $str($CONDITIONAL_geno.geno_MOD_0_0):
2093 '${CONDITIONAL_geno.geno_MOD_0_0}'
2094 #end if
2095
2096 #if $str($CONDITIONAL_geno.CONDITIONAL_geno_MOD_1.CONDITIONAL_SELECT_geno_MOD_1) == 'from_list'
2097 '${CONDITIONAL_geno.CONDITIONAL_geno_MOD_1.geno_MOD_1}'
2098 #end if
2099
2100
2101 #end if
2102
2103 #if str($CONDITIONAL_mind.CONDITIONAL_SELECT_mind) == "set":
2104 --mind
2105
2106
2107 #if $str($CONDITIONAL_mind.mind_MOD_0_0):
2108 '${CONDITIONAL_mind.mind_MOD_0_0}'
2109 #end if
2110
2111 #if $str($CONDITIONAL_mind.CONDITIONAL_mind_MOD_1.CONDITIONAL_SELECT_mind_MOD_1) == 'from_list'
2112 '${CONDITIONAL_mind.CONDITIONAL_mind_MOD_1.mind_MOD_1}'
2113 #end if
2114
2115
2116 #end if
2117
2118 #if str($CONDITIONAL_require_pheno.CONDITIONAL_SELECT_require_pheno) == "set":
2119 --require-pheno
2120
2121
2122 #if $str($CONDITIONAL_require_pheno.require_pheno_MOD_0_0):
2123 '${CONDITIONAL_require_pheno.require_pheno_MOD_0_0}'
2124 #end if
2125
2126 #end if
2127
2128 #if str($CONDITIONAL_require_covar.CONDITIONAL_SELECT_require_covar) == "set":
2129 --require-covar
2130
2131
2132 #if $str($CONDITIONAL_require_covar.require_covar_MOD_0_0):
2133 '${CONDITIONAL_require_covar.require_covar_MOD_0_0}'
2134 #end if
2135
2136 #end if
2137
2138 #if str($CONDITIONAL_maf.CONDITIONAL_SELECT_maf) == "set":
2139 --maf
2140
2141
2142 #if $str($CONDITIONAL_maf.maf_MOD_0_0):
2143 '${CONDITIONAL_maf.maf_MOD_0_0}'
2144 #end if
2145
2146 #if $str($CONDITIONAL_maf.maf_MOD_1_0):
2147 '${CONDITIONAL_maf.maf_MOD_1_0}'
2148 #end if
2149
2150 #end if
2151
2152 #if str($CONDITIONAL_max_maf.CONDITIONAL_SELECT_max_maf) == "set":
2153 --max-maf
2154
2155
2156 #if $str($CONDITIONAL_max_maf.max_maf_MOD_0_0):
2157 '${CONDITIONAL_max_maf.max_maf_MOD_0_0}'
2158 #end if
2159
2160 #if $str($CONDITIONAL_max_maf.max_maf_MOD_1_0):
2161 '${CONDITIONAL_max_maf.max_maf_MOD_1_0}'
2162 #end if
2163
2164 #end if
2165
2166 #if str($CONDITIONAL_mac.CONDITIONAL_SELECT_mac) == "set":
2167 --mac
2168
2169
2170 #if $str($CONDITIONAL_mac.mac_MOD_0_0):
2171 '${CONDITIONAL_mac.mac_MOD_0_0}'
2172 #end if
2173
2174 #if $str($CONDITIONAL_mac.mac_MOD_1_0):
2175 '${CONDITIONAL_mac.mac_MOD_1_0}'
2176 #end if
2177
2178 #end if
2179
2180 #if str($CONDITIONAL_max_mac.CONDITIONAL_SELECT_max_mac) == "set":
2181 --max-mac
2182
2183
2184 #if $str($CONDITIONAL_max_mac.max_mac_MOD_0_0):
2185 '${CONDITIONAL_max_mac.max_mac_MOD_0_0}'
2186 #end if
2187
2188 #if $str($CONDITIONAL_max_mac.max_mac_MOD_1_0):
2189 '${CONDITIONAL_max_mac.max_mac_MOD_1_0}'
2190 #end if
2191
2192 #end if
2193
2194 #if str($CONDITIONAL_maf_succ.CONDITIONAL_SELECT_maf_succ) == "set":
2195 --maf-succ
2196
2197
2198 #end if
2199
2200 #if str($CONDITIONAL_min_alleles.CONDITIONAL_SELECT_min_alleles) == "set":
2201 --min-alleles
2202
2203
2204 #if $str($CONDITIONAL_min_alleles.min_alleles_MOD_0_0):
2205 '${CONDITIONAL_min_alleles.min_alleles_MOD_0_0}'
2206 #end if
2207
2208 #end if
2209
2210 #if str($CONDITIONAL_max_alleles.CONDITIONAL_SELECT_max_alleles) == "set":
2211 --max-alleles
2212
2213
2214 #if $str($CONDITIONAL_max_alleles.max_alleles_MOD_0_0):
2215 '${CONDITIONAL_max_alleles.max_alleles_MOD_0_0}'
2216 #end if
2217
2218 #end if
2219
2220 #if str($CONDITIONAL_read_freq.CONDITIONAL_SELECT_read_freq) == "set":
2221 --read-freq
2222
2223
2224 #if $str($CONDITIONAL_read_freq.read_freq_MOD_0_0):
2225 '${CONDITIONAL_read_freq.read_freq_MOD_0_0}'
2226 #end if
2227
2228 #end if
2229
2230 #if str($CONDITIONAL_hwe.CONDITIONAL_SELECT_hwe) == "set":
2231 --hwe
2232
2233
2234 #if $str($CONDITIONAL_hwe.hwe_MOD_0_0):
2235 '${CONDITIONAL_hwe.hwe_MOD_0_0}'
2236 #end if
2237
2238 #if $str($CONDITIONAL_hwe.hwe_MOD_1_0):
2239 '${CONDITIONAL_hwe.hwe_MOD_1_0}'
2240 #end if
2241
2242 #if $str($CONDITIONAL_hwe.hwe_MOD_2_0):
2243 '${CONDITIONAL_hwe.hwe_MOD_2_0}'
2244 #end if
2245
2246 #end if
2247
2248 #if str($CONDITIONAL_mach_r2_filter.CONDITIONAL_SELECT_mach_r2_filter) == "set":
2249 --mach-r2-filter
2250
2251
2252 #if $str($CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_0_0):
2253 '${CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_0_0}'
2254 #end if
2255
2256 #if $str($CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_1_0):
2257 '${CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_1_0}'
2258 #end if
2259
2260 #end if
2261
2262 #if str($CONDITIONAL_minimac3_r2_filter.CONDITIONAL_SELECT_minimac3_r2_filter) == "set":
2263 --minimac3-r2-filter
2264
2265
2266 #if $str($CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_0_0):
2267 '${CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_0_0}'
2268 #end if
2269
2270 #if $str($CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_1_0):
2271 '${CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_1_0}'
2272 #end if
2273
2274 #end if
2275
2276 #if str($CONDITIONAL_keep_females.CONDITIONAL_SELECT_keep_females) == "set":
2277 --keep-females
2278
2279
2280 #end if
2281
2282 #if str($CONDITIONAL_keep_males.CONDITIONAL_SELECT_keep_males) == "set":
2283 --keep-males
2284
2285
2286 #end if
2287
2288 #if str($CONDITIONAL_keep_nosex.CONDITIONAL_SELECT_keep_nosex) == "set":
2289 --keep-nosex
2290
2291
2292 #end if
2293
2294 #if str($CONDITIONAL_remove_females.CONDITIONAL_SELECT_remove_females) == "set":
2295 --remove-females
2296
2297
2298 #end if
2299
2300 #if str($CONDITIONAL_remove_males.CONDITIONAL_SELECT_remove_males) == "set":
2301 --remove-males
2302
2303
2304 #end if
2305
2306 #if str($CONDITIONAL_remove_nosex.CONDITIONAL_SELECT_remove_nosex) == "set":
2307 --remove-nosex
2308
2309
2310 #end if
2311
2312 #if str($CONDITIONAL_keep_founders.CONDITIONAL_SELECT_keep_founders) == "set":
2313 --keep-founders
2314
2315
2316 #end if
2317
2318 #if str($CONDITIONAL_keep_nonfounders.CONDITIONAL_SELECT_keep_nonfounders) == "set":
2319 --keep-nonfounders
2320
2321
2322 #end if
2323
2324 #if str($CONDITIONAL_keep_if.CONDITIONAL_SELECT_keep_if) == "set":
2325 --keep-if
2326
2327
2328 #if $str($CONDITIONAL_keep_if.keep_if_MOD_0_0):
2329 '${CONDITIONAL_keep_if.keep_if_MOD_0_0}'
2330 #end if
2331
2332 #if $str($CONDITIONAL_keep_if.keep_if_MOD_1_0):
2333 '${CONDITIONAL_keep_if.keep_if_MOD_1_0}'
2334 #end if
2335
2336 #if $str($CONDITIONAL_keep_if.keep_if_MOD_2_0):
2337 '${CONDITIONAL_keep_if.keep_if_MOD_2_0}'
2338 #end if
2339
2340 #end if
2341
2342 #if str($CONDITIONAL_remove_if.CONDITIONAL_SELECT_remove_if) == "set":
2343 --remove-if
2344
2345
2346 #if $str($CONDITIONAL_remove_if.remove_if_MOD_0_0):
2347 '${CONDITIONAL_remove_if.remove_if_MOD_0_0}'
2348 #end if
2349
2350 #if $str($CONDITIONAL_remove_if.remove_if_MOD_1_0):
2351 '${CONDITIONAL_remove_if.remove_if_MOD_1_0}'
2352 #end if
2353
2354 #if $str($CONDITIONAL_remove_if.remove_if_MOD_2_0):
2355 '${CONDITIONAL_remove_if.remove_if_MOD_2_0}'
2356 #end if
2357
2358 #end if
2359
2360 #if str($CONDITIONAL_nonfounders.CONDITIONAL_SELECT_nonfounders) == "set":
2361 --nonfounders
2362
2363
2364 #end if
2365
2366 #if str($CONDITIONAL_bad_freqs.CONDITIONAL_SELECT_bad_freqs) == "set":
2367 --bad-freqs
2368
2369
2370 #end if
2371
2372 #if str($CONDITIONAL_export_allele.CONDITIONAL_SELECT_export_allele) == "set":
2373 --export-allele
2374
2375
2376 #if $str($CONDITIONAL_export_allele.export_allele_MOD_0_0):
2377 '${CONDITIONAL_export_allele.export_allele_MOD_0_0}'
2378 #end if
2379
2380 #end if
2381
2382 #if str($CONDITIONAL_output_chr.CONDITIONAL_SELECT_output_chr) == "set":
2383 --output-chr
2384
2385
2386 #if $str($CONDITIONAL_output_chr.output_chr_MOD_0_0):
2387 '${CONDITIONAL_output_chr.output_chr_MOD_0_0}'
2388 #end if
2389
2390 #end if
2391
2392 #if str($CONDITIONAL_output_missing_genotype.CONDITIONAL_SELECT_output_missing_genotype) == "set":
2393 --output-missing-genotype
2394
2395
2396 #if $str($CONDITIONAL_output_missing_genotype.output_missing_genotype_MOD_0_0):
2397 '${CONDITIONAL_output_missing_genotype.output_missing_genotype_MOD_0_0}'
2398 #end if
2399
2400 #end if
2401
2402 #if str($CONDITIONAL_output_missing_phenotype.CONDITIONAL_SELECT_output_missing_phenotype) == "set":
2403 --output-missing-phenotype
2404
2405
2406 #if $str($CONDITIONAL_output_missing_phenotype.output_missing_phenotype_MOD_0_0):
2407 '${CONDITIONAL_output_missing_phenotype.output_missing_phenotype_MOD_0_0}'
2408 #end if
2409
2410 #end if
2411
2412 #if str($CONDITIONAL_sort_vars.CONDITIONAL_SELECT_sort_vars) == "set":
2413 --sort-vars
2414
2415
2416 #if $str($CONDITIONAL_sort_vars.sort_vars_MOD_0_0):
2417 '${CONDITIONAL_sort_vars.sort_vars_MOD_0_0}'
2418 #end if
2419
2420 #end if
2421
2422 #if str($CONDITIONAL_set_hh_missing.CONDITIONAL_SELECT_set_hh_missing) == "set":
2423 --set-hh-missing
2424
2425
2426 #if $str($CONDITIONAL_set_hh_missing.set_hh_missing_MOD_0_0):
2427 '${CONDITIONAL_set_hh_missing.set_hh_missing_MOD_0_0}'
2428 #end if
2429
2430 #end if
2431
2432 #if str($CONDITIONAL_set_mixed_mt_missing.CONDITIONAL_SELECT_set_mixed_mt_missing) == "set":
2433 --set-mixed-mt-missing
2434
2435
2436 #if $str($CONDITIONAL_set_mixed_mt_missing.set_mixed_mt_missing_MOD_0_0):
2437 '${CONDITIONAL_set_mixed_mt_missing.set_mixed_mt_missing_MOD_0_0}'
2438 #end if
2439
2440 #end if
2441
2442 #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_OVERLOADED_SELECT_split_par) == "form_0":
2443 #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.CONDITIONAL_SELECT_split_par) == "set":
2444 --split-par
2445
2446 #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0):
2447 '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0}'
2448 #end if
2449 #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0):
2450 '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0}'
2451 #end if
2452 #end if
2453 #end if
2454
2455 #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_OVERLOADED_SELECT_split_par) == "form_1":
2456 #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.CONDITIONAL_SELECT_split_par) == "set":
2457 --split-par
2458
2459 #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0):
2460 '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0}'
2461 #end if
2462 #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0):
2463 '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0}'
2464 #end if
2465 #end if
2466 #end if
2467
2468 #if str($CONDITIONAL_merge_par.CONDITIONAL_SELECT_merge_par) == "set":
2469 --merge-par
2470
2471
2472 #end if
2473
2474 #if str($CONDITIONAL_merge_x.CONDITIONAL_SELECT_merge_x) == "set":
2475 --merge-x
2476
2477
2478 #end if
2479
2480 #if str($CONDITIONAL_set_missing_var_ids.CONDITIONAL_SELECT_set_missing_var_ids) == "set":
2481 --set-missing-var-ids
2482
2483
2484 #if $str($CONDITIONAL_set_missing_var_ids.set_missing_var_ids_MOD_0_0):
2485 '${CONDITIONAL_set_missing_var_ids.set_missing_var_ids_MOD_0_0}'
2486 #end if
2487
2488 #end if
2489
2490 #if str($CONDITIONAL_set_all_var_ids.CONDITIONAL_SELECT_set_all_var_ids) == "set":
2491 --set-all-var-ids
2492
2493
2494 #if $str($CONDITIONAL_set_all_var_ids.set_all_var_ids_MOD_0_0):
2495 '${CONDITIONAL_set_all_var_ids.set_all_var_ids_MOD_0_0}'
2496 #end if
2497
2498 #end if
2499
2500 #if str($CONDITIONAL_var_id_multi.CONDITIONAL_SELECT_var_id_multi) == "set":
2501 --var-id-multi
2502
2503
2504 #if $str($CONDITIONAL_var_id_multi.var_id_multi_MOD_0_0):
2505 '${CONDITIONAL_var_id_multi.var_id_multi_MOD_0_0}'
2506 #end if
2507
2508 #end if
2509
2510 #if str($CONDITIONAL_var_id_multi_nonsnp.CONDITIONAL_SELECT_var_id_multi_nonsnp) == "set":
2511 --var-id-multi-nonsnp
2512
2513
2514 #if $str($CONDITIONAL_var_id_multi_nonsnp.var_id_multi_nonsnp_MOD_0_0):
2515 '${CONDITIONAL_var_id_multi_nonsnp.var_id_multi_nonsnp_MOD_0_0}'
2516 #end if
2517
2518 #end if
2519
2520 #if str($CONDITIONAL_new_id_max_allele_len.CONDITIONAL_SELECT_new_id_max_allele_len) == "set":
2521 --new-id-max-allele-len
2522
2523
2524 #if $str($CONDITIONAL_new_id_max_allele_len.new_id_max_allele_len_MOD_0_0):
2525 '${CONDITIONAL_new_id_max_allele_len.new_id_max_allele_len_MOD_0_0}'
2526 #end if
2527
2528 #if $str($CONDITIONAL_new_id_max_allele_len.CONDITIONAL_new_id_max_allele_len_MOD_1.CONDITIONAL_SELECT_new_id_max_allele_len_MOD_1) == 'from_list'
2529 '${CONDITIONAL_new_id_max_allele_len.CONDITIONAL_new_id_max_allele_len_MOD_1.new_id_max_allele_len_MOD_1}'
2530 #end if
2531
2532
2533 #end if
2534
2535 #if str($CONDITIONAL_missing_var_code.CONDITIONAL_SELECT_missing_var_code) == "set":
2536 --missing-var-code
2537
2538
2539 #if $str($CONDITIONAL_missing_var_code.missing_var_code_MOD_0_0):
2540 '${CONDITIONAL_missing_var_code.missing_var_code_MOD_0_0}'
2541 #end if
2542
2543 #end if
2544
2545 #if str($CONDITIONAL_update_map.CONDITIONAL_SELECT_update_map) == "set":
2546 --update-map
2547
2548
2549 #if $CONDITIONAL_update_map.update_map_MOD_0_0:
2550 '${CONDITIONAL_update_map.update_map_MOD_0_0}'
2551 #end if
2552
2553 #if $str($CONDITIONAL_update_map.update_map_MOD_1_0):
2554 '${CONDITIONAL_update_map.update_map_MOD_1_0}'
2555 #end if
2556
2557 #if $str($CONDITIONAL_update_map.update_map_MOD_2_0):
2558 '${CONDITIONAL_update_map.update_map_MOD_2_0}'
2559 #end if
2560
2561 #if $str($CONDITIONAL_update_map.update_map_MOD_3_0):
2562 '${CONDITIONAL_update_map.update_map_MOD_3_0}'
2563 #end if
2564
2565 #end if
2566
2567 #if str($CONDITIONAL_update_name.CONDITIONAL_SELECT_update_name) == "set":
2568 --update-name
2569
2570
2571 #if $CONDITIONAL_update_name.update_name_MOD_0_0:
2572 '${CONDITIONAL_update_name.update_name_MOD_0_0}'
2573 #end if
2574
2575 #if $str($CONDITIONAL_update_name.update_name_MOD_1_0):
2576 '${CONDITIONAL_update_name.update_name_MOD_1_0}'
2577 #end if
2578
2579 #if $str($CONDITIONAL_update_name.update_name_MOD_2_0):
2580 '${CONDITIONAL_update_name.update_name_MOD_2_0}'
2581 #end if
2582
2583 #if $str($CONDITIONAL_update_name.update_name_MOD_3_0):
2584 '${CONDITIONAL_update_name.update_name_MOD_3_0}'
2585 #end if
2586
2587 #end if
2588
2589 #if str($CONDITIONAL_recover_var_ids.CONDITIONAL_SELECT_recover_var_ids) == "set":
2590 --recover-var-ids
2591
2592
2593 #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_0_0):
2594 '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_0_0}'
2595 #end if
2596
2597 #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_1_0):
2598 '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_1_0}'
2599 #end if
2600
2601 #if $str($CONDITIONAL_recover_var_ids.CONDITIONAL_recover_var_ids_MOD_2.CONDITIONAL_SELECT_recover_var_ids_MOD_2) == 'from_list'
2602 '${CONDITIONAL_recover_var_ids.CONDITIONAL_recover_var_ids_MOD_2.recover_var_ids_MOD_2}'
2603 #end if
2604
2605
2606 #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_3_0):
2607 '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_3_0}'
2608 #end if
2609
2610 #end if
2611
2612 #if str($CONDITIONAL_update_alleles.CONDITIONAL_SELECT_update_alleles) == "set":
2613 --update-alleles
2614
2615
2616 #if $CONDITIONAL_update_alleles.update_alleles_MOD_0_0:
2617 '${CONDITIONAL_update_alleles.update_alleles_MOD_0_0}'
2618 #end if
2619
2620 #end if
2621
2622 #if str($CONDITIONAL_update_ids.CONDITIONAL_SELECT_update_ids) == "set":
2623 --update-ids
2624
2625
2626 #if $CONDITIONAL_update_ids.update_ids_MOD_0_0:
2627 '${CONDITIONAL_update_ids.update_ids_MOD_0_0}'
2628 #end if
2629
2630 #end if
2631
2632 #if str($CONDITIONAL_update_parents.CONDITIONAL_SELECT_update_parents) == "set":
2633 --update-parents
2634
2635
2636 #if $CONDITIONAL_update_parents.update_parents_MOD_0_0:
2637 '${CONDITIONAL_update_parents.update_parents_MOD_0_0}'
2638 #end if
2639
2640 #end if
2641
2642 #if str($CONDITIONAL_update_sex.CONDITIONAL_SELECT_update_sex) == "set":
2643 --update-sex
2644
2645
2646 #if $CONDITIONAL_update_sex.update_sex_MOD_0_0:
2647 '${CONDITIONAL_update_sex.update_sex_MOD_0_0}'
2648 #end if
2649
2650 #if $str($CONDITIONAL_update_sex.update_sex_MOD_1_0):
2651 '${CONDITIONAL_update_sex.update_sex_MOD_1_0}'
2652 #end if
2653
2654 #if $str($CONDITIONAL_update_sex.update_sex_MOD_2_0):
2655 '${CONDITIONAL_update_sex.update_sex_MOD_2_0}'
2656 #end if
2657
2658 #end if
2659
2660 #if str($CONDITIONAL_real_ref_alleles.CONDITIONAL_SELECT_real_ref_alleles) == "set":
2661 --real-ref-alleles
2662
2663
2664 #end if
2665
2666 #if str($CONDITIONAL_maj_ref.CONDITIONAL_SELECT_maj_ref) == "set":
2667 --maj-ref
2668
2669
2670 #if $str($CONDITIONAL_maj_ref.maj_ref_MOD_0_0):
2671 '${CONDITIONAL_maj_ref.maj_ref_MOD_0_0}'
2672 #end if
2673
2674 #end if
2675
2676 #if str($CONDITIONAL_ref_allele.CONDITIONAL_SELECT_ref_allele) == "set":
2677 --ref-allele
2678
2679
2680 #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_0_0):
2681 '${CONDITIONAL_ref_allele.ref_allele_MOD_0_0}'
2682 #end if
2683
2684 #if $CONDITIONAL_ref_allele.ref_allele_MOD_1_0:
2685 '${CONDITIONAL_ref_allele.ref_allele_MOD_1_0}'
2686 #end if
2687
2688 #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_2_0):
2689 '${CONDITIONAL_ref_allele.ref_allele_MOD_2_0}'
2690 #end if
2691
2692 #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_3_0):
2693 '${CONDITIONAL_ref_allele.ref_allele_MOD_3_0}'
2694 #end if
2695
2696 #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_4_0):
2697 '${CONDITIONAL_ref_allele.ref_allele_MOD_4_0}'
2698 #end if
2699
2700 #end if
2701
2702 #if str($CONDITIONAL_alt1_allele.CONDITIONAL_SELECT_alt1_allele) == "set":
2703 --alt1-allele
2704
2705
2706 #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_0_0):
2707 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_0_0}'
2708 #end if
2709
2710 #if $CONDITIONAL_alt1_allele.alt1_allele_MOD_1_0:
2711 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_1_0}'
2712 #end if
2713
2714 #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_2_0):
2715 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_2_0}'
2716 #end if
2717
2718 #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_3_0):
2719 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_3_0}'
2720 #end if
2721
2722 #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_4_0):
2723 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_4_0}'
2724 #end if
2725
2726 #end if
2727
2728 #if str($CONDITIONAL_ref_from_fa.CONDITIONAL_SELECT_ref_from_fa) == "set":
2729 --ref-from-fa
2730
2731
2732 #if $str($CONDITIONAL_ref_from_fa.ref_from_fa_MOD_0_0):
2733 '${CONDITIONAL_ref_from_fa.ref_from_fa_MOD_0_0}'
2734 #end if
2735
2736 #end if
2737
2738 #if str($CONDITIONAL_normalize.CONDITIONAL_SELECT_normalize) == "set":
2739 --normalize
2740
2741
2742 #if $str($CONDITIONAL_normalize.normalize_MOD_0_0):
2743 '${CONDITIONAL_normalize.normalize_MOD_0_0}'
2744 #end if
2745
2746 #end if
2747
2748 #if str($CONDITIONAL_indiv_sort.CONDITIONAL_SELECT_indiv_sort) == "set":
2749 --indiv-sort
2750
2751
2752 #if $str($CONDITIONAL_indiv_sort.indiv_sort_MOD_0_0):
2753 '${CONDITIONAL_indiv_sort.indiv_sort_MOD_0_0}'
2754 #end if
2755
2756 #if $CONDITIONAL_indiv_sort.indiv_sort_MOD_1_0:
2757 '${CONDITIONAL_indiv_sort.indiv_sort_MOD_1_0}'
2758 #end if
2759
2760 #end if
2761
2762 #if str($CONDITIONAL_king_table_filter.CONDITIONAL_SELECT_king_table_filter) == "set":
2763 --king-table-filter
2764
2765
2766 #if $str($CONDITIONAL_king_table_filter.king_table_filter_MOD_0_0):
2767 '${CONDITIONAL_king_table_filter.king_table_filter_MOD_0_0}'
2768 #end if
2769
2770 #end if
2771
2772 #if str($CONDITIONAL_king_table_subset.CONDITIONAL_SELECT_king_table_subset) == "set":
2773 --king-table-subset
2774
2775
2776 #if $CONDITIONAL_king_table_subset.king_table_subset_MOD_0_0:
2777 '${CONDITIONAL_king_table_subset.king_table_subset_MOD_0_0}'
2778 #end if
2779
2780 #if $str($CONDITIONAL_king_table_subset.king_table_subset_MOD_1_0):
2781 '${CONDITIONAL_king_table_subset.king_table_subset_MOD_1_0}'
2782 #end if
2783
2784 #end if
2785
2786 #if str($CONDITIONAL_condition.CONDITIONAL_SELECT_condition) == "set":
2787 --condition
2788
2789
2790 #if $str($CONDITIONAL_condition.condition_MOD_0_0):
2791 '${CONDITIONAL_condition.condition_MOD_0_0}'
2792 #end if
2793
2794 #if $str($CONDITIONAL_condition.CONDITIONAL_condition_MOD_1.CONDITIONAL_SELECT_condition_MOD_1) == 'from_list'
2795 '${CONDITIONAL_condition.CONDITIONAL_condition_MOD_1.condition_MOD_1}'
2796 #end if
2797
2798
2799 #if $str($CONDITIONAL_condition.condition_MOD_2_0):
2800 '${CONDITIONAL_condition.condition_MOD_2_0}'
2801 #end if
2802
2803 #end if
2804
2805 #if str($CONDITIONAL_condition_list.CONDITIONAL_SELECT_condition_list) == "set":
2806 --condition-list
2807
2808
2809 #if $CONDITIONAL_condition_list.condition_list_MOD_0_0:
2810 '${CONDITIONAL_condition_list.condition_list_MOD_0_0}'
2811 #end if
2812
2813 #if $str($CONDITIONAL_condition_list.CONDITIONAL_condition_list_MOD_1.CONDITIONAL_SELECT_condition_list_MOD_1) == 'from_list'
2814 '${CONDITIONAL_condition_list.CONDITIONAL_condition_list_MOD_1.condition_list_MOD_1}'
2815 #end if
2816
2817
2818 #if $str($CONDITIONAL_condition_list.condition_list_MOD_2_0):
2819 '${CONDITIONAL_condition_list.condition_list_MOD_2_0}'
2820 #end if
2821
2822 #end if
2823
2824 #if str($CONDITIONAL_parameters.CONDITIONAL_SELECT_parameters) == "set":
2825 --parameters
2826
2827
2828 #if $str($CONDITIONAL_parameters.parameters_MOD_0_0):
2829 '${CONDITIONAL_parameters.parameters_MOD_0_0}'
2830 #end if
2831
2832 #end if
2833
2834 #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_OVERLOADED_SELECT_tests) == "form_0":
2835 #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.CONDITIONAL_SELECT_tests) == "set":
2836 --tests
2837
2838 #if $str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.tests_MOD_0_0):
2839 '${CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.tests_MOD_0_0}'
2840 #end if
2841 #end if
2842 #end if
2843
2844 #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_OVERLOADED_SELECT_tests) == "form_1":
2845 #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.CONDITIONAL_SELECT_tests) == "set":
2846 --tests
2847
2848 #end if
2849 #end if
2850
2851 #if str($CONDITIONAL_vif.CONDITIONAL_SELECT_vif) == "set":
2852 --vif
2853
2854
2855 #if $str($CONDITIONAL_vif.vif_MOD_0_0):
2856 '${CONDITIONAL_vif.vif_MOD_0_0}'
2857 #end if
2858
2859 #end if
2860
2861 #if str($CONDITIONAL_max_corr.CONDITIONAL_SELECT_max_corr) == "set":
2862 --max-corr
2863
2864
2865 #if $str($CONDITIONAL_max_corr.max_corr_MOD_0_0):
2866 '${CONDITIONAL_max_corr.max_corr_MOD_0_0}'
2867 #end if
2868
2869 #end if
2870
2871 #if str($CONDITIONAL_xchr_model.CONDITIONAL_SELECT_xchr_model) == "set":
2872 --xchr-model
2873
2874
2875 #if $str($CONDITIONAL_xchr_model.xchr_model_MOD_0_0):
2876 '${CONDITIONAL_xchr_model.xchr_model_MOD_0_0}'
2877 #end if
2878
2879 #end if
2880
2881 #if str($CONDITIONAL_adjust.CONDITIONAL_SELECT_adjust) == "set":
2882 --adjust
2883
2884
2885 #if $str($CONDITIONAL_adjust.adjust_MOD_0_0):
2886 '${CONDITIONAL_adjust.adjust_MOD_0_0}'
2887 #end if
2888
2889 #if $str($CONDITIONAL_adjust.adjust_MOD_1_0):
2890 '${CONDITIONAL_adjust.adjust_MOD_1_0}'
2891 #end if
2892
2893 #if $str($CONDITIONAL_adjust.adjust_MOD_2_0):
2894 '${CONDITIONAL_adjust.adjust_MOD_2_0}'
2895 #end if
2896
2897 #if $str($CONDITIONAL_adjust.adjust_MOD_3_0):
2898 '${CONDITIONAL_adjust.adjust_MOD_3_0}'
2899 #end if
2900
2901 #end if
2902
2903 #if str($CONDITIONAL_lambda.CONDITIONAL_SELECT_lambda) == "set":
2904 --lambda
2905
2906
2907 #end if
2908
2909 #if str($CONDITIONAL_adjust_chr_field.CONDITIONAL_SELECT_adjust_chr_field) == "set":
2910 --adjust-chr-field
2911
2912
2913 #if $str($CONDITIONAL_adjust_chr_field.adjust_chr_field_MOD_0_0):
2914 '${CONDITIONAL_adjust_chr_field.adjust_chr_field_MOD_0_0}'
2915 #end if
2916
2917 #end if
2918
2919 #if str($CONDITIONAL_adjust_pos_field.CONDITIONAL_SELECT_adjust_pos_field) == "set":
2920 --adjust-pos-field
2921
2922
2923 #if $str($CONDITIONAL_adjust_pos_field.adjust_pos_field_MOD_0_0):
2924 '${CONDITIONAL_adjust_pos_field.adjust_pos_field_MOD_0_0}'
2925 #end if
2926
2927 #end if
2928
2929 #if str($CONDITIONAL_adjust_id_field.CONDITIONAL_SELECT_adjust_id_field) == "set":
2930 --adjust-id-field
2931
2932
2933 #if $str($CONDITIONAL_adjust_id_field.adjust_id_field_MOD_0_0):
2934 '${CONDITIONAL_adjust_id_field.adjust_id_field_MOD_0_0}'
2935 #end if
2936
2937 #end if
2938
2939 #if str($CONDITIONAL_adjust_ref_field.CONDITIONAL_SELECT_adjust_ref_field) == "set":
2940 --adjust-ref-field
2941
2942
2943 #if $str($CONDITIONAL_adjust_ref_field.adjust_ref_field_MOD_0_0):
2944 '${CONDITIONAL_adjust_ref_field.adjust_ref_field_MOD_0_0}'
2945 #end if
2946
2947 #end if
2948
2949 #if str($CONDITIONAL_adjust_alt_field.CONDITIONAL_SELECT_adjust_alt_field) == "set":
2950 --adjust-alt-field
2951
2952
2953 #if $str($CONDITIONAL_adjust_alt_field.adjust_alt_field_MOD_0_0):
2954 '${CONDITIONAL_adjust_alt_field.adjust_alt_field_MOD_0_0}'
2955 #end if
2956
2957 #end if
2958
2959 #if str($CONDITIONAL_adjust_a1_field.CONDITIONAL_SELECT_adjust_a1_field) == "set":
2960 --adjust-a1-field
2961
2962
2963 #if $str($CONDITIONAL_adjust_a1_field.adjust_a1_field_MOD_0_0):
2964 '${CONDITIONAL_adjust_a1_field.adjust_a1_field_MOD_0_0}'
2965 #end if
2966
2967 #end if
2968
2969 #if str($CONDITIONAL_adjust_test_field.CONDITIONAL_SELECT_adjust_test_field) == "set":
2970 --adjust-test-field
2971
2972
2973 #if $str($CONDITIONAL_adjust_test_field.adjust_test_field_MOD_0_0):
2974 '${CONDITIONAL_adjust_test_field.adjust_test_field_MOD_0_0}'
2975 #end if
2976
2977 #end if
2978
2979 #if str($CONDITIONAL_adjust_p_field.CONDITIONAL_SELECT_adjust_p_field) == "set":
2980 --adjust-p-field
2981
2982
2983 #if $str($CONDITIONAL_adjust_p_field.adjust_p_field_MOD_0_0):
2984 '${CONDITIONAL_adjust_p_field.adjust_p_field_MOD_0_0}'
2985 #end if
2986
2987 #end if
2988
2989 #if str($CONDITIONAL_ci.CONDITIONAL_SELECT_ci) == "set":
2990 --ci
2991
2992
2993 #if $str($CONDITIONAL_ci.ci_MOD_0_0):
2994 '${CONDITIONAL_ci.ci_MOD_0_0}'
2995 #end if
2996
2997 #end if
2998
2999 #if str($CONDITIONAL_pfilter.CONDITIONAL_SELECT_pfilter) == "set":
3000 --pfilter
3001
3002
3003 #if $str($CONDITIONAL_pfilter.pfilter_MOD_0_0):
3004 '${CONDITIONAL_pfilter.pfilter_MOD_0_0}'
3005 #end if
3006
3007 #end if
3008
3009 #if str($CONDITIONAL_score_col_nums.CONDITIONAL_SELECT_score_col_nums) == "set":
3010 --score-col-nums
3011
3012
3013 #if $str($CONDITIONAL_score_col_nums.score_col_nums_MOD_0_0):
3014 '${CONDITIONAL_score_col_nums.score_col_nums_MOD_0_0}'
3015 #end if
3016
3017 #end if
3018
3019 #if str($CONDITIONAL_q_score_range.CONDITIONAL_SELECT_q_score_range) == "set":
3020 --q-score-range
3021
3022
3023 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_0_0):
3024 '${CONDITIONAL_q_score_range.q_score_range_MOD_0_0}'
3025 #end if
3026
3027 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_1_0):
3028 '${CONDITIONAL_q_score_range.q_score_range_MOD_1_0}'
3029 #end if
3030
3031 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_2_0):
3032 '${CONDITIONAL_q_score_range.q_score_range_MOD_2_0}'
3033 #end if
3034
3035 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_3_0):
3036 '${CONDITIONAL_q_score_range.q_score_range_MOD_3_0}'
3037 #end if
3038
3039 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_4_0):
3040 '${CONDITIONAL_q_score_range.q_score_range_MOD_4_0}'
3041 #end if
3042
3043 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_5_0):
3044 '${CONDITIONAL_q_score_range.q_score_range_MOD_5_0}'
3045 #end if
3046
3047 #end if
3048
3049 #if str($CONDITIONAL_vscore_col_nums.CONDITIONAL_SELECT_vscore_col_nums) == "set":
3050 --vscore-col-nums
3051
3052
3053 #if $str($CONDITIONAL_vscore_col_nums.vscore_col_nums_MOD_0_0):
3054 '${CONDITIONAL_vscore_col_nums.vscore_col_nums_MOD_0_0}'
3055 #end if
3056
3057 #end if
3058
3059 #if str($CONDITIONAL_memory.CONDITIONAL_SELECT_memory) == "set":
3060 --memory
3061
3062
3063 #if $str($CONDITIONAL_memory.memory_MOD_0_0):
3064 '${CONDITIONAL_memory.memory_MOD_0_0}'
3065 #end if
3066
3067 #if $str($CONDITIONAL_memory.memory_MOD_1_0):
3068 '${CONDITIONAL_memory.memory_MOD_1_0}'
3069 #end if
3070
3071 #end if
3072
3073 #if str($CONDITIONAL_threads.CONDITIONAL_SELECT_threads) == "set":
3074 --threads
3075
3076
3077 #if $str($CONDITIONAL_threads.threads_MOD_0_0):
3078 '${CONDITIONAL_threads.threads_MOD_0_0}'
3079 #end if
3080
3081 #end if
3082
3083 #if str($CONDITIONAL_d.CONDITIONAL_SELECT_d) == "set":
3084 --d
3085
3086
3087 #if $str($CONDITIONAL_d.d_MOD_0_0):
3088 '${CONDITIONAL_d.d_MOD_0_0}'
3089 #end if
3090
3091 #end if
3092
3093 #if str($CONDITIONAL_seed.CONDITIONAL_SELECT_seed) == "set":
3094 --seed
3095
3096
3097 #if $str($CONDITIONAL_seed.seed_MOD_0_0):
3098 '${CONDITIONAL_seed.seed_MOD_0_0}'
3099 #end if
3100
3101 #end if
3102
3103 #if str($CONDITIONAL_output_min_p.CONDITIONAL_SELECT_output_min_p) == "set":
3104 --output-min-p
3105
3106
3107 #if $str($CONDITIONAL_output_min_p.output_min_p_MOD_0_0):
3108 '${CONDITIONAL_output_min_p.output_min_p_MOD_0_0}'
3109 #end if
3110
3111 #end if
3112
3113 #if str($CONDITIONAL_debug.CONDITIONAL_SELECT_debug) == "set":
3114 --debug
3115
3116
3117 #end if
3118
3119 #if str($CONDITIONAL_randmem.CONDITIONAL_SELECT_randmem) == "set":
3120 --randmem
3121
3122
3123 #end if
3124
3125 #if str($CONDITIONAL_warning_errcode.CONDITIONAL_SELECT_warning_errcode) == "set":
3126 --warning-errcode
3127
3128
3129 #end if
3130
3131 #if str($CONDITIONAL_zst_level.CONDITIONAL_SELECT_zst_level) == "set":
3132 --zst-level
3133
3134
3135 #if $str($CONDITIONAL_zst_level.zst_level_MOD_0_0):
3136 '${CONDITIONAL_zst_level.zst_level_MOD_0_0}'
3137 #end if
3138
3139 #end if
3140 ]]></command>
3141 <inputs>
3142 <conditional name="CONDITIONAL_pfile">
3143 <param name="CONDITIONAL_SELECT_pfile" type="select" label="Set Pfile" help="Specify .pgen + .pvar[.zst] + .psam prefix. " argument="--pfile">
3144 <option value="no_set" selected="True">Don't set</option>
3145 <option value="set">Set value(s)</option>
3146 </param>
3147 <when value="no_set">
3148 </when>
3149 <when value="set">
3150
3151 <param name="pfile_MOD_0_0" type="text" label="prefix" value="" optional="True" argument="prefix" help=""/>
3152 <param name="pfile_MOD_1_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
3153 </when>
3154 </conditional>
3155 <conditional name="CONDITIONAL_pgen">
3156 <param name="CONDITIONAL_SELECT_pgen" type="select" label="Set Pgen" help="Specify full name of .pgen/.bed file. " argument="--pgen">
3157 <option value="no_set" selected="True">Don't set</option>
3158 <option value="set">Set value(s)</option>
3159 </param>
3160 <when value="no_set">
3161 </when>
3162 <when value="set">
3163
3164 <param name="pgen_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
3165 </when>
3166 </conditional>
3167 <conditional name="CONDITIONAL_pvar">
3168 <param name="CONDITIONAL_SELECT_pvar" type="select" label="Set Pvar" help="Specify full name of .pvar/.bim file. " argument="--pvar">
3169 <option value="no_set" selected="True">Don't set</option>
3170 <option value="set">Set value(s)</option>
3171 </param>
3172 <when value="no_set">
3173 </when>
3174 <when value="set">
3175
3176 <param name="pvar_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
3177 </when>
3178 </conditional>
3179 <conditional name="CONDITIONAL_psam">
3180 <param name="CONDITIONAL_SELECT_psam" type="select" label="Set Psam" help="Specify full name of .psam/.fam file. " argument="--psam">
3181 <option value="no_set" selected="True">Don't set</option>
3182 <option value="set">Set value(s)</option>
3183 </param>
3184 <when value="no_set">
3185 </when>
3186 <when value="set">
3187
3188 <param name="psam_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
3189 </when>
3190 </conditional>
3191 <conditional name="CONDITIONAL_bpfile">
3192 <param name="CONDITIONAL_SELECT_bpfile" type="select" label="Set Bpfile" help="Specify .pgen + .bim[.zst] + .fam prefix. " argument="--bpfile">
3193 <option value="no_set" selected="True">Don't set</option>
3194 <option value="set">Set value(s)</option>
3195 </param>
3196 <when value="no_set">
3197 </when>
3198 <when value="set">
3199
3200 <param name="bpfile_MOD_0_0" type="text" label="prefix" value="" optional="True" argument="prefix" help=""/>
3201 <param name="bpfile_MOD_1_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
3202 </when>
3203 </conditional>
3204 <conditional name="CONDITIONAL_keep_autoconv">
3205 <param name="CONDITIONAL_SELECT_keep_autoconv" type="select" label="Set Keep autoconv" help="When importing non-PLINK-binary data, don't delete autogenerated binary fileset at end of run. " argument="--keep-autoconv">
3206 <option value="no_set" selected="True">Don't set</option>
3207 <option value="set">Set value(s)</option>
3208 </param>
3209 <when value="no_set">
3210 </when>
3211 <when value="set">
3212
3213 </when>
3214 </conditional>
3215 <conditional name="CONDITIONAL_no_fid">
3216 <param name="CONDITIONAL_SELECT_no_fid" type="select" label="Set No fid" help=".fam file does not contain column 1 (family ID). " argument="--no-fid">
3217 <option value="no_set" selected="True">Don't set</option>
3218 <option value="set">Set value(s)</option>
3219 </param>
3220 <when value="no_set">
3221 </when>
3222 <when value="set">
3223
3224 </when>
3225 </conditional>
3226 <conditional name="CONDITIONAL_no_parents">
3227 <param name="CONDITIONAL_SELECT_no_parents" type="select" label="Set No parents" help=".fam file does not contain columns 3-4 (parents). " argument="--no-parents">
3228 <option value="no_set" selected="True">Don't set</option>
3229 <option value="set">Set value(s)</option>
3230 </param>
3231 <when value="no_set">
3232 </when>
3233 <when value="set">
3234
3235 </when>
3236 </conditional>
3237 <conditional name="CONDITIONAL_no_sex">
3238 <param name="CONDITIONAL_SELECT_no_sex" type="select" label="Set No sex" help=".fam file does not contain column 5 (sex). " argument="--no-sex">
3239 <option value="no_set" selected="True">Don't set</option>
3240 <option value="set">Set value(s)</option>
3241 </param>
3242 <when value="no_set">
3243 </when>
3244 <when value="set">
3245
3246 </when>
3247 </conditional>
3248 <conditional name="CONDITIONAL_vcf">
3249 <param name="CONDITIONAL_SELECT_vcf" type="select" label="Set Vcf" help="" argument="--vcf">
3250 <option value="no_set" selected="True">Don't set</option>
3251 <option value="set">Set value(s)</option>
3252 </param>
3253 <when value="no_set">
3254 </when>
3255 <when value="set">
3256
3257 <param name="vcf_MOD_0_0" type="data" format="vcf" label="filename" multiple="False" optional="True" argument="filename"/>
3258 <param name="vcf_MOD_1_0" type="text" label="'dosage='&lt;field&gt;" value="" optional="False" argument="'dosage='&lt;field&gt;" help=""/>
3259 </when>
3260 </conditional>
3261 <conditional name="CONDITIONAL_bcf">
3262 <param name="CONDITIONAL_SELECT_bcf" type="select" label="Set Bcf" help="Specify full name of .vcf{|.gz|.zst} or BCF2 file to import. * These can be used with --psam/--fam. * By default, dosage information is not imported. To import the GP field (must be VCFv4.3-style 0..1, one probability per possible genotype), add 'dosage=GP' (or 'dosage=GP-force', see below). To import Minimac3-style DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else for now) causes the named field to be interpreted as a Minimac3-style dosage. Note that, in the dosage=GP case, PLINK 2 collapses the probabilities down to dosages; you cannot use PLINK 2 to losslessly convert VCF FORMAT:GP data to e.g. BGEN format. To make this more obvious, PLINK 2 now errors out when dosage=GP is used on a file with a FORMAT:DS header line and --import-dosage-certainty wasn't specified, since dosage=DS extracts the same information more quickly in this situation. You can suppress this error with 'dosage=GP-force'. In all of these cases, hardcalls are regenerated from scratch from the dosages. As a consequence, variants with no GT field can now be imported; they will be assumed to contain only diploid calls when HDS is also absent." argument="--bcf">
3263 <option value="no_set" selected="True">Don't set</option>
3264 <option value="set">Set value(s)</option>
3265 </param>
3266 <when value="no_set">
3267 </when>
3268 <when value="set">
3269
3270 <param name="bcf_MOD_0_0" type="data" format="bcf" label="filename" multiple="False" optional="True" argument="filename"/>
3271 <param name="bcf_MOD_1_0" type="text" label="'dosage='&lt;field&gt;" value="" optional="False" argument="'dosage='&lt;field&gt;" help=""/>
3272 </when>
3273 </conditional>
3274 <conditional name="CONDITIONAL_bgen">
3275 <param name="CONDITIONAL_SELECT_bgen" type="select" label="Set Bgen" help="" argument="--bgen">
3276 <option value="no_set" selected="True">Don't set</option>
3277 <option value="set">Set value(s)</option>
3278 </param>
3279 <when value="no_set">
3280 </when>
3281 <when value="set">
3282
3283 <param name="bgen_MOD_0_0" type="data" format="plink.bgen" label="filename" multiple="False" optional="True" argument="filename"/>
3284 <param name="bgen_MOD_1_0" type="text" label="REF/ALT mode" value="" optional="False" argument="REF/ALT mode" help=""/>
3285 <param name="bgen_MOD_2_0" type="text" label="'snpid-chr'" value="" optional="False" argument="'snpid-chr'" help=""/>
3286 </when>
3287 </conditional>
3288 <conditional name="CONDITIONAL_gen">
3289 <param name="CONDITIONAL_SELECT_gen" type="select" label="Set Gen" help="" argument="--gen">
3290 <option value="no_set" selected="True">Don't set</option>
3291 <option value="set">Set value(s)</option>
3292 </param>
3293 <when value="no_set">
3294 </when>
3295 <when value="set">
3296
3297 <param name="gen_MOD_0_0" type="data" format="plink.gen" label="filename" multiple="False" optional="True" argument="filename"/>
3298 <param name="gen_MOD_1_0" type="text" label="REF/ALT mode" value="" optional="False" argument="REF/ALT mode" help=""/>
3299 </when>
3300 </conditional>
3301 <conditional name="CONDITIONAL_sample">
3302 <param name="CONDITIONAL_SELECT_sample" type="select" label="Set Sample" help="Specify an Oxford-format dataset to import. --data specifies a .gen[.zst] + .sample pair, while --bgen specifies a BGEN v1.1+ file. * If a BGEN v1.2+ file contains sample IDs, it may be imported without a companion .sample file. * With 'snpid-chr', chromosome codes are read from the 'SNP ID' field instead of the usual chromosome field. * The following REF/ALT modes are supported: 'ref-first': The first allele for each variant is REF. 'ref-last': The last allele for each variant is REF. 'ref-unknown' (default): The last allele for each variant is treated as provisional-REF. This parameter will be required instead of optional in alpha 3." argument="--sample">
3303 <option value="no_set" selected="True">Don't set</option>
3304 <option value="set">Set value(s)</option>
3305 </param>
3306 <when value="no_set">
3307 </when>
3308 <when value="set">
3309
3310 <param name="sample_MOD_0_0" type="data" format="plink.sample" label="filename" multiple="False" optional="True" argument="filename"/>
3311 </when>
3312 </conditional>
3313 <conditional name="CONDITIONAL_haps">
3314 <param name="CONDITIONAL_SELECT_haps" type="select" label="Set Haps" help="" argument="--haps">
3315 <option value="no_set" selected="True">Don't set</option>
3316 <option value="set">Set value(s)</option>
3317 </param>
3318 <when value="no_set">
3319 </when>
3320 <when value="set">
3321
3322 <param name="haps_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
3323 <conditional name="CONDITIONAL_haps_MOD_1">
3324 <param name="CONDITIONAL_SELECT_haps_MOD_1" type="select" label="How to set Haps">
3325 <option value="no_set" selected="True">Don't set</option>
3326 <option value="from_list">Select from list</option>
3327
3328 </param>
3329 <when value="no_set">
3330 </when>
3331
3332 <when value="from_list">
3333 <param name="haps_MOD_1" type="select" label="Select value">
3334 <option value="{ref-first">{ref-first</option>
3335 <option value="ref-last}">ref-last}</option>
3336 </param>
3337 </when>
3338 </conditional>
3339 </when>
3340 </conditional>
3341 <conditional name="CONDITIONAL_legend">
3342 <param name="CONDITIONAL_SELECT_legend" type="select" label="Set Legend" help="Specify .haps [+ .legend] file(s) to import. * When --legend is specified, it's assumed that the --haps file doesn't contain header columns. * On chrX, the second male column may contain dummy '-' entries. (However, PLINK 2 currently cannot handle omitted male columns.) * If not used with --sample, new sample IDs are of the form 'per#/per#'." argument="--legend">
3343 <option value="no_set" selected="True">Don't set</option>
3344 <option value="set">Set value(s)</option>
3345 </param>
3346 <when value="no_set">
3347 </when>
3348 <when value="set">
3349
3350 <param name="legend_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
3351 <param name="legend_MOD_1_0" type="text" label="chr code" value="" optional="True" argument="chr code" help=""/>
3352 </when>
3353 </conditional>
3354 <conditional name="CONDITIONAL_map">
3355 <param name="CONDITIONAL_SELECT_map" type="select" label="Set Map" help="Specify full name of .map file. " argument="--map">
3356 <option value="no_set" selected="True">Don't set</option>
3357 <option value="set">Set value(s)</option>
3358 </param>
3359 <when value="no_set">
3360 </when>
3361 <when value="set">
3362
3363 <param name="map_MOD_0_0" type="data" format="plink.map" label="filename" multiple="False" optional="True" argument="filename"/>
3364 </when>
3365 </conditional>
3366 <conditional name="CONDITIONAL_import_dosage">
3367 <param name="CONDITIONAL_SELECT_import_dosage" type="select" label="Set Import dosage" help="Specify PLINK 1.x-style dosage file to import. * You must also specify a companion .psam/.fam file. * By default, PLINK assumes that the file contains a header line, which has 'SNP' in (1-based) column i+1, 'A1' in column i+j+2, 'A2' in column i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are normally zero, but can be changed with 'skip0', 'skip1', and 'skip2' respectively. FID/IID are normally assumed to be separate tokens, but if they're merged into a single token you can specify the delimiter with 'id-delim='.) If such a header line is not present, use the 'noheader' modifier; samples will then be assumed to appear in the same order as they do in the .psam/.fam file. * You may specify a companion .map file. If you do not, * 'single-chr=' can be used to specify that all variants are on the named chromosome. Otherwise, you can use 'chr-col-num=' to read chromosome codes from the given (1-based) column number. * 'pos-col-num=' causes bp coordinates to be read from the given column number. * The 'format=' modifier lets you specify the number of values used to represent each dosage. 'format=1' normally indicates a single 0..2 A1 expected count; 'dose1' modifies this to a 0..1 frequency. 'format=2' indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het likelihood. 'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2. 'format=infer' (the default) infers the format from the number of columns in the first nonheader line." argument="--import-dosage">
3368 <option value="no_set" selected="True">Don't set</option>
3369 <option value="set">Set value(s)</option>
3370 </param>
3371 <when value="no_set">
3372 </when>
3373 <when value="set">
3374
3375 <param name="import_dosage_MOD_0_0" type="text" label="allele dosage file" value="" optional="True" argument="allele dosage file" help=""/>
3376 <param name="import_dosage_MOD_1_0" type="text" label="'noheader'" value="" optional="False" argument="'noheader'" help=""/>
3377 <param name="import_dosage_MOD_2_0" type="text" label="'id-delim='&lt;char&gt;" value="" optional="False" argument="'id-delim='&lt;char&gt;" help=""/>
3378 <param name="import_dosage_MOD_3_0" type="text" label="'skip0='&lt;i&gt;" value="" optional="False" argument="'skip0='&lt;i&gt;" help=""/>
3379 <param name="import_dosage_MOD_4_0" type="text" label="'skip1='&lt;j&gt;" value="" optional="False" argument="'skip1='&lt;j&gt;" help=""/>
3380 <param name="import_dosage_MOD_5_0" type="text" label="'skip2='&lt;k&gt;" value="" optional="False" argument="'skip2='&lt;k&gt;" help=""/>
3381 <param name="import_dosage_MOD_6_0" type="text" label="'dose1'" value="" optional="False" argument="'dose1'" help=""/>
3382 <param name="import_dosage_MOD_7_0" type="text" label="'format='&lt;m&gt;" value="" optional="False" argument="'format='&lt;m&gt;" help=""/>
3383 <conditional name="CONDITIONAL_import_dosage_MOD_8">
3384 <param name="CONDITIONAL_SELECT_import_dosage_MOD_8" type="select" label="How to set Import dosage">
3385 <option value="no_set" selected="True">Don't set</option>
3386 <option value="from_list">Select from list</option>
3387
3388 </param>
3389 <when value="no_set">
3390 </when>
3391
3392 <when value="from_list">
3393 <param name="import_dosage_MOD_8" type="select" label="Select value">
3394 <option value="{ref-first">{ref-first</option>
3395 <option value="ref-last}">ref-last}</option>
3396 </param>
3397 </when>
3398 </conditional>
3399 <param name="import_dosage_MOD_9_0" type="text" label="'single-chr='&lt;code&gt;" value="" optional="False" argument="'single-chr='&lt;code&gt;" help=""/>
3400 <param name="import_dosage_MOD_10_0" type="text" label="'chr-col-num='&lt;#&gt;" value="" optional="False" argument="'chr-col-num='&lt;#&gt;" help=""/>
3401 <param name="import_dosage_MOD_11_0" type="text" label="'pos-col-num='&lt;#&gt;" value="" optional="False" argument="'pos-col-num='&lt;#&gt;" help=""/>
3402 </when>
3403 </conditional>
3404 <conditional name="CONDITIONAL_dummy">
3405 <param name="CONDITIONAL_SELECT_dummy" type="select" label="Set Dummy" help="This generates a fake input dataset with the specified number of samples and SNPs. * By default, the missing dosage and phenotype frequencies are zero. These can be changed by providing 3rd and 4th numeric parameters. * By default, allele codes are As and Bs; this can be changed with the 'acgt', '1234', or '12' modifier. * By default, one binary phenotype is generated. 'pheno-ct=' can be used to change the number of phenotypes, and 'scalar-pheno' causes these phenotypes to be normally distributed scalars. * By default, all (nonmissing) dosages are in {0,1,2}. To make some of them take on decimal values, use 'dosage-freq='. (These dosages are affected by --hard-call-threshold and --dosage-erase-threshold.)" argument="--dummy">
3406 <option value="no_set" selected="True">Don't set</option>
3407 <option value="set">Set value(s)</option>
3408 </param>
3409 <when value="no_set">
3410 </when>
3411 <when value="set">
3412
3413 <param name="dummy_MOD_0_0" type="text" label="sample ct" value="" optional="True" argument="sample ct" help=""/>
3414 <param name="dummy_MOD_1_0" type="text" label="SNP ct" value="" optional="True" argument="SNP ct" help=""/>
3415 <param name="dummy_MOD_2_0" type="text" label="missing dosage freq" value="" optional="False" argument="missing dosage freq" help=""/>
3416 <param name="dummy_MOD_3_0" type="text" label="missing pheno freq" value="" optional="False" argument="missing pheno freq" help=""/>
3417 <conditional name="CONDITIONAL_dummy_MOD_4">
3418 <param name="CONDITIONAL_SELECT_dummy_MOD_4" type="select" label="How to set Dummy">
3419 <option value="no_set" selected="True">Don't set</option>
3420 <option value="from_list">Select from list</option>
3421
3422 </param>
3423 <when value="no_set">
3424 </when>
3425
3426 <when value="from_list">
3427 <param name="dummy_MOD_4" type="select" label="Select value">
3428 <option value="{acgt">{acgt</option>
3429 <option value="1234">1234</option>
3430 <option value="12}">12}</option>
3431 </param>
3432 </when>
3433 </conditional>
3434 <param name="dummy_MOD_5_0" type="text" label="'pheno-ct='&lt;count&gt;" value="" optional="False" argument="'pheno-ct='&lt;count&gt;" help=""/>
3435 <param name="dummy_MOD_6_0" type="text" label="'scalar-pheno'" value="" optional="False" argument="'scalar-pheno'" help=""/>
3436 <param name="dummy_MOD_7_0" type="text" label="'dosage-freq='&lt;rate&gt;" value="" optional="False" argument="'dosage-freq='&lt;rate&gt;" help=""/>
3437 </when>
3438 </conditional>
3439 <conditional name="CONDITIONAL_fa">
3440 <param name="CONDITIONAL_SELECT_fa" type="select" label="Set Fa" help="Specify full name of reference FASTA file. " argument="--fa">
3441 <option value="no_set" selected="True">Don't set</option>
3442 <option value="set">Set value(s)</option>
3443 </param>
3444 <when value="no_set">
3445 </when>
3446 <when value="set">
3447
3448 <param name="fa_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
3449 </when>
3450 </conditional>
3451 <conditional name="CONDITIONAL_rm_dup">
3452 <param name="CONDITIONAL_SELECT_rm_dup" type="select" label="Set Rm dup" help="Remove all but one instance of each duplicate-ID variant (ignoring the missing ID), and (with the 'list' modifier) write a list of duplicated IDs to &lt;output prefix&gt;.rmdup.list. The following modes of operation are supported: * 'error' (default) causes this to error out when there's a genotype data or other mismatch between the records. A list of affected IDs is written to &lt;output prefix&gt;.rmdup.mismatch. * 'retain-mismatch' causes all instances of a duplicate-ID variant to be retained when there's a genotype data or variant info mismatch; otherwise one instance is kept. The .rmdup.mismatch file is also written. * 'exclude-mismatch' removes all instances of duplicate-ID mismatched variants instead. * 'exclude-all' causes all instances of duplicate-ID variants to be removed, even when the actual records are identical. * 'force-first' causes only the first instance of duplicate-ID variants to be kept, under all circumstances." argument="--rm-dup">
3453 <option value="no_set" selected="True">Don't set</option>
3454 <option value="set">Set value(s)</option>
3455 </param>
3456 <when value="no_set">
3457 </when>
3458 <when value="set">
3459
3460 <param name="rm_dup_MOD_0_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
3461 <param name="rm_dup_MOD_1_0" type="text" label="'list'" value="" optional="False" argument="'list'" help=""/>
3462 </when>
3463 </conditional>
3464 <conditional name="CONDITIONAL_make_pgen">
3465 <param name="CONDITIONAL_SELECT_make_pgen" type="select" label="Set Make pgen" help="" argument="--make-pgen">
3466 <option value="no_set" selected="True">Don't set</option>
3467 <option value="set">Set value(s)</option>
3468 </param>
3469 <when value="no_set">
3470 </when>
3471 <when value="set">
3472
3473 <param name="make_pgen_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
3474 <param name="make_pgen_MOD_1_0" type="text" label="'format='&lt;code&gt;" value="" optional="False" argument="'format='&lt;code&gt;" help=""/>
3475 <param name="make_pgen_MOD_2_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/>
3476 <param name="make_pgen_MOD_3_0" type="text" label="'erase-phase'" value="" optional="False" argument="'erase-phase'" help=""/>
3477 <param name="make_pgen_MOD_4_0" type="text" label="'erase-dosage'" value="" optional="False" argument="'erase-dosage'" help=""/>
3478 <param name="make_pgen_MOD_5_0" type="text" label="'pvar-cols='&lt;col set descriptor&gt;" value="" optional="False" argument="'pvar-cols='&lt;col set descriptor&gt;" help=""/>
3479 <param name="make_pgen_MOD_6_0" type="text" label="'psam-cols='&lt;col set descriptor&gt;" value="" optional="False" argument="'psam-cols='&lt;col set descriptor&gt;" help=""/>
3480 </when>
3481 </conditional>
3482 <conditional name="CONDITIONAL_make_bpgen">
3483 <param name="CONDITIONAL_SELECT_make_bpgen" type="select" label="Set Make bpgen" help="" argument="--make-bpgen">
3484 <option value="no_set" selected="True">Don't set</option>
3485 <option value="set">Set value(s)</option>
3486 </param>
3487 <when value="no_set">
3488 </when>
3489 <when value="set">
3490
3491 <param name="make_bpgen_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
3492 <param name="make_bpgen_MOD_1_0" type="text" label="'format='&lt;code&gt;" value="" optional="False" argument="'format='&lt;code&gt;" help=""/>
3493 <param name="make_bpgen_MOD_2_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/>
3494 <param name="make_bpgen_MOD_3_0" type="text" label="'erase-phase'" value="" optional="False" argument="'erase-phase'" help=""/>
3495 <param name="make_bpgen_MOD_4_0" type="text" label="'erase-dosage'" value="" optional="False" argument="'erase-dosage'" help=""/>
3496 </when>
3497 </conditional>
3498 <conditional name="CONDITIONAL_make_bed">
3499 <param name="CONDITIONAL_SELECT_make_bed" type="select" label="Set Make bed" help="Create a new PLINK binary fileset (--make-pgen = .pgen + .pvar[.zst] + .psam, --make-bpgen = .pgen + .bim[.zst] + .fam). * Unlike the automatic text-to-binary converters (which only heed chromosome filters), this supports all of PLINK's filtering flags. * The 'vzs' modifier causes the variant file (.pvar/.bim) to be Zstd-compressed. * The 'format' modifier requests an uncompressed fixed-variant-width .pgen file. (These do not directly support multiallelic variants.) The following format code is currently supported: 2: just like .bed, except with an extended (12-byte instead of 3-byte) header containing variant/sample counts, and rotated genotype codes (00 = hom ref, 01 = het, 10 = hom alt, 11 = missing). * The 'erase-phase' and 'erase-dosage' modifiers prevent phase and dosage information from being written to the new .pgen. * The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT. Supported optional .pvar column sets are: xheader: All ## header lines (yeah, this is technically not a column), except for possibly FILTER/INFO definitions when those column(s) have been removed. Without this, only the #CHROM header line is kept. maybequal: QUAL. Omitted if all remaining values are missing. qual: Force QUAL column to be written even when empty. maybefilter: FILTER. Omitted if all remaining values are missing. filter: Force FILTER column to be written even when empty. maybeinfo: INFO. Omitted if all remaining values are missing, or if INFO:PR is the only subfield. info: Force INFO column to be written. maybecm: Centimorgan coordinate. Omitted if all remaining values = 0. cm: Force CM column to be written even when empty. The default is xheader,maybequal,maybefilter,maybeinfo,maybecm. * Supported column sets for the .psam file are: maybefid: Family ID, '0' = missing. Omitted if all values missing. fid: Force FID column to be written even when empty. maybesid: Source ID, '0' = missing. Omitted if all values missing. sid: Force SID column to be written even when empty. maybeparents: Father and mother IIDs. Omitted if all values missing. parents: Force PAT and MAT columns to be written even when empty. sex: '1' = male, '2' = female, 'NA' = missing. pheno1: First active phenotype. If none, all column entries are set to the --output-missing-phenotype string. phenos: All active phenotypes, if any. (Can be combined with pheno1 to force at least one phenotype column to be written.) The default is maybefid,maybesid,maybeparents,sex,phenos." argument="--make-bed">
3500 <option value="no_set" selected="True">Don't set</option>
3501 <option value="set">Set value(s)</option>
3502 </param>
3503 <when value="no_set">
3504 </when>
3505 <when value="set">
3506
3507 <param name="make_bed_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
3508 <param name="make_bed_MOD_1_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/>
3509 </when>
3510 </conditional>
3511 <conditional name="CONDITIONAL_make_just_pvar">
3512 <param name="CONDITIONAL_SELECT_make_just_pvar" type="select" label="Set Make just pvar" help="" argument="--make-just-pvar">
3513 <option value="no_set" selected="True">Don't set</option>
3514 <option value="set">Set value(s)</option>
3515 </param>
3516 <when value="no_set">
3517 </when>
3518 <when value="set">
3519
3520 <param name="make_just_pvar_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3521 <param name="make_just_pvar_MOD_1_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
3522 </when>
3523 </conditional>
3524 <conditional name="CONDITIONAL_make_just_psam">
3525 <param name="CONDITIONAL_SELECT_make_just_psam" type="select" label="Set Make just psam" help="" argument="--make-just-psam">
3526 <option value="no_set" selected="True">Don't set</option>
3527 <option value="set">Set value(s)</option>
3528 </param>
3529 <when value="no_set">
3530 </when>
3531 <when value="set">
3532
3533 <param name="make_just_psam_MOD_0_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
3534 </when>
3535 </conditional>
3536 <conditional name="CONDITIONAL_make_just_bim">
3537 <param name="CONDITIONAL_SELECT_make_just_bim" type="select" label="Set Make just bim" help="" argument="--make-just-bim">
3538 <option value="no_set" selected="True">Don't set</option>
3539 <option value="set">Set value(s)</option>
3540 </param>
3541 <when value="no_set">
3542 </when>
3543 <when value="set">
3544
3545 <param name="make_just_bim_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3546 </when>
3547 </conditional>
3548 <param name="make_just_fam" type="boolean" label="Make just fam" truevalue="--make-just-fam" falsevalue="" optional="true" argument="--make-just-fam" help="Variants of --make-pgen/--make-bed which only write a new variant or sample file. These don't always require an input genotype file. USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary genotype data and your sample/variant indexes if you use these commands improperly. If you have any doubt, stick with --make-[b]pgen/--make-bed." checked="False"/>
3549 <conditional name="CONDITIONAL_export">
3550 <param name="CONDITIONAL_SELECT_export" type="select" label="Set Export" help="Create a new fileset with all filters applied. The following output formats are supported: (actually, only A, AD, A-transpose, bgen-1.x, ind-major-bed, haps, hapslegend, oxford, and vcf are implemented for now) * '23': 23andMe 4-column format. This can only be used on a single sample's data (--keep may be handy), and does not support multicharacter allele codes. * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R. If you need uncounted alleles to be named in the header line, add the 'include-alt' modifier. * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding. Also supports 'include-alt'. * 'A-transpose': Variant-major 0/1/2. * 'beagle': Unphased per-autosome .dat and .map files, readable by early BEAGLE versions. * 'beagle-nomap': Single .beagle.dat file. * 'bgen-1.x': Oxford-format .bgen + .sample. For v1.2/v1.3, sample identifiers are stored in the .bgen (with id-delim and id-paste settings applied), and default precision is 16-bit (use the 'bits' modifier to reduce this). * 'bimbam': Regular BIMBAM format. * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file. Does not support multiple chromosomes. * 'fastphase': Per-chromosome fastPHASE files, with .chr-&lt;chr #&gt;.phase.inp filename extensions. * 'fastphase-1chr': Single .phase.inp file. Does not support multiple chromosomes. * 'haps', 'hapslegend': Oxford-format .haps + .sample[ + .legend]. All data must be biallelic and phased. When the 'bgz' modifier is present, the .haps file is block-gzipped. * 'HV': Per-chromosome Haploview files, with .chr-&lt;chr #&gt;{.ped,.info} filename extensions. * 'HV-1chr': Single Haploview .ped + .info file pair. Does not support multiple chromosomes. * 'ind-major-bed': PLINK 1 sample-major .bed (+ .bim + .fam). * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile. * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile + --reference. * 'list': Single genotype-based list, up to 4 lines per variant. To omit nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y' modifier. * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a genotype-based list which omits the most common genotype for each variant. Also supports 'omit-nonmale-y'. * 'oxford': Oxford-format .gen + .sample. When the 'bgz' modifier is present, the .gen file is block-gzipped. * 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file. * 'compound-genotypes': Same as 'ped', except that the space between each pair of same-variant allele codes is removed. * 'structure': Structure-format. * 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with --tfile. * 'vcf', 'vcf-4.2': VCF (default version 4.3). If PAR1 and PAR2 are present, they are automatically merged with chrX, with proper handling of chromosome codes and male ploidy. When the 'bgz' modifier is present, the VCF file is block-gzipped. The 'id-paste' modifier controls which .psam columns are used to construct sample IDs (choices are maybefid, fid, iid, maybesid, and sid; default is maybefid,iid,maybesid), while the 'id-delim' modifier sets the character between the ID pieces (default '_'). Dosages are not exported unless the 'vcf-dosage=' modifier is present. The following five dosage export modes are supported: 'GP': genotype posterior probabilities (v4.3 only). 'DS': Minimac3-style dosages, omitted for hardcalls. 'DS-force': Minimac3-style dosages, never omit. 'HDS': Minimac3-style phased dosages, omitted for hardcalls and unphased calls. Also includes 'DS' output. 'HDS-force': Always report DS and HDS. In addition, * The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles to be coded as '2', while '01' maps alt1 -&gt; 0 and ref -&gt; 1. * The 'spaces' modifier makes the output space-delimited instead of tab-delimited, whenever both are permitted. * For biallelic formats where it's unspecified whether the reference/major allele should appear first or second, --export defaults to second for compatibility with PLINK 1.9. Use 'ref-first' to change this. (Note that this doesn't apply to the 'A', 'AD', and 'A-transpose' formats; use --export-allele to control which alleles are counted there.)" argument="--export">
3551 <option value="no_set" selected="True">Don't set</option>
3552 <option value="set">Set value(s)</option>
3553 </param>
3554 <when value="no_set">
3555 </when>
3556 <when value="set">
3557
3558 <param name="export_MOD_0_0" type="text" label="output format(s)..." value="" optional="True" argument="output format(s)..." help="Multiple values are allowed"/>
3559 <conditional name="CONDITIONAL_export_MOD_1">
3560 <param name="CONDITIONAL_SELECT_export_MOD_1" type="select" label="How to set Export">
3561 <option value="no_set" selected="True">Don't set</option>
3562 <option value="from_list">Select from list</option>
3563
3564 </param>
3565 <when value="no_set">
3566 </when>
3567
3568 <when value="from_list">
3569 <param name="export_MOD_1" type="select" label="Select value">
3570 <option value="{01">{01</option>
3571 <option value="12}">12}</option>
3572 </param>
3573 </when>
3574 </conditional>
3575 <param name="export_MOD_2_0" type="text" label="'bgz'" value="" optional="False" argument="'bgz'" help=""/>
3576 <param name="export_MOD_3_0" type="text" label="'id-delim='&lt;char&gt;" value="" optional="False" argument="'id-delim='&lt;char&gt;" help=""/>
3577 <param name="export_MOD_4_0" type="text" label="'id-paste='&lt;column set descriptor&gt;" value="" optional="False" argument="'id-paste='&lt;column set descriptor&gt;" help=""/>
3578 <param name="export_MOD_5_0" type="text" label="'include-alt'" value="" optional="False" argument="'include-alt'" help=""/>
3579 <param name="export_MOD_6_0" type="text" label="'omit-nonmale-y'" value="" optional="False" argument="'omit-nonmale-y'" help=""/>
3580 <param name="export_MOD_7_0" type="text" label="'spaces'" value="" optional="False" argument="'spaces'" help=""/>
3581 <param name="export_MOD_8_0" type="text" label="'vcf-dosage='&lt;field&gt;" value="" optional="False" argument="'vcf-dosage='&lt;field&gt;" help=""/>
3582 <param name="export_MOD_9_0" type="text" label="'ref-first'" value="" optional="False" argument="'ref-first'" help=""/>
3583 <param name="export_MOD_10_0" type="text" label="'bits='&lt;#&gt;" value="" optional="False" argument="'bits='&lt;#&gt;" help=""/>
3584 </when>
3585 </conditional>
3586 <conditional name="CONDITIONAL_freq">
3587 <param name="CONDITIONAL_SELECT_freq" type="select" label="Set Freq" help="['refbins='&lt;comma-separated bin boundaries&gt; | 'refbins-file='&lt;file&gt;] ['alt1bins='&lt;comma-separated bin boundaries&gt; | 'alt1bins-file='&lt;file&gt;] Empirical allele frequency report. By default, only founders are considered. Dosages are taken into account (e.g. heterozygous haploid calls count as 0.5). Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. reffreq: Reference allele frequency/dosage. alt1freq: Alt1 frequency/dosage. altfreq: Comma-separated frequencies/dosages for all alternate alleles. freq: Similar to altfreq, except ref is also included at the start. eq: Comma-separated &lt;allele&gt;=&lt;freq&gt; for all present alleles. (If no alleles are present, the column contains a single '.'.) eqz: Same as eq, except zero-counts are included. alteq/alteqz: Same as eq/eqz, except reference allele is omitted. numeq: 0=&lt;freq&gt;,1=&lt;freq&gt;, etc. Zero-counts are omitted. altnumeq: Same as numeq, except reference allele is omitted. machr2: Unphased MaCH imputation quality metric. minimac3r2: Phased Minimac3 imputation quality. nobs: Number of allele observations. The default is chrom,ref,alt,altfreq,nobs. Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with 'counts') file(s) are generated when 'refbins='/'refbins-file=' or 'alt1bins='/'alt1bins-file=' is present; these report the total number of frequencies or counts in each left-closed, right-open interval. (If you only want these histogram(s), and not the main report, add 'bins-only'.)" argument="--freq">
3588 <option value="no_set" selected="True">Don't set</option>
3589 <option value="set">Set value(s)</option>
3590 </param>
3591 <when value="no_set">
3592 </when>
3593 <when value="set">
3594
3595 <param name="freq_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3596 <param name="freq_MOD_1_0" type="text" label="'counts'" value="" optional="False" argument="'counts'" help=""/>
3597 <param name="freq_MOD_2_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
3598 <param name="freq_MOD_3_0" type="text" label="'bins-only'" value="" optional="False" argument="'bins-only'" help=""/>
3599 </when>
3600 </conditional>
3601 <conditional name="CONDITIONAL_geno_counts">
3602 <param name="CONDITIONAL_SELECT_geno_counts" type="select" label="Set Geno counts" help="Variant-based hardcall genotype count report (considering both alleles simultaneously in the diploid case). Nonfounders are now included; use --keep-founders if this is a problem. Heterozygous haploid calls are treated as missing. Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. homref: Homozygous-ref count. refalt1: Heterozygous ref-alt1 count. refalt: Comma-separated het ref-altx counts. homalt1: Homozygous-alt1 count. altxy: Comma-separated altx-alty counts, in (1/1)-(1/2)-(2/2)-(1/3)-... order. xy: Similar to altxy, except the reference allele is treated as alt0, and the sequence starts (0/0)-(0/1)-(1/1)-(0/2)-... hapref: Haploid-ref count. hapalt1: Haploid-alt1 count. hapalt: Comma-separated haploid-altx counts. hap: Similar to hapalts, except ref is also included at the start. numeq: 0/0=&lt;hom ref ct&gt;,0/1=&lt;het ref-alt1&gt;,1/1=&lt;hom alt1&gt;,...,0=&lt;hap ref&gt; etc. Zero-counts are omitted. (If all genotypes are missing, the column contains a single '.'.) missing: Number of missing genotypes. nobs: Number of (nonmissing) genotype observations. The default is chrom,ref,alt,homref,refalt,altxy,hapref,hapalt,missing." argument="--geno-counts">
3603 <option value="no_set" selected="True">Don't set</option>
3604 <option value="set">Set value(s)</option>
3605 </param>
3606 <when value="no_set">
3607 </when>
3608 <when value="set">
3609
3610 <param name="geno_counts_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3611 <param name="geno_counts_MOD_1_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
3612 </when>
3613 </conditional>
3614 <conditional name="CONDITIONAL_sample_counts">
3615 <param name="CONDITIONAL_SELECT_sample_counts" type="select" label="Set Sample counts" help="Sample-based hardcall genotype count report. * Unknown-sex samples are treated as female. * Heterozygous haploid calls (MT included) are treated as missing. * As with other PLINK 2 commands, SNPs that have not been left-normalized are counted as non-SNP non-symbolic. (Use e.g. --normalize when that's a problem.) * Supported column sets are: maybefid: FID, if that column was present in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was present in the input. sid: Force SID column to be written even when absent in the input. sex: '1' = male, '2' = female, 'NA' = missing. hom: Homozygous genotype count. homref: Homozygous-ref genotype count. homalt: Homozygous-alt genotype count. homaltsnp: Homozygous-alt SNP count. het: Heterozygous genotype count. refalt: Heterozygous ref-altx genotype count. het2alt: Heterozygous altx-alty genotype count. hetsnp: Heterozygous SNP count. dipts: Diploid SNP transition count. ts: SNP transition count (excluding chrY for females). diptv: Diploid SNP transversion count. tv: SNP transversion count. dipnonsnpsymb: Diploid non-SNP, non-symbolic count. nonsnpsymb: Non-SNP, non-symbolic count. symbolic: Symbolic variant count. nonsnp: Non-SNP count. dipsingle: Number of singletons relative to this dataset, across just diploid calls. (Note that if the ALT allele in a chrX biallelic variant appears in exactly one female and one male, that counts as a singleton for just the female.) single: Number of singletons relative to this dataset. haprefwfemaley: Haploid-ref count, counting chrY for everyone. hapref: Haploid-ref count, excluding chrY for females. hapaltwfemaley: Haploid-alt count, counting chrY for everyone. hapalt: Haploid-alt count, excluding chrY for females. missingwfemaley: Missing call count, counting chrY for everyone. missing: Missing call count, excluding chrY for females. The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv, dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley. * The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb', 'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous altx-alty call separately, since they can be of different subtypes. (I.e. if they are of the same subtype, the corresponding count is incremented by 2.) As a consequence, these columns are unaffected by variant split/join." argument="--sample-counts">
3616 <option value="no_set" selected="True">Don't set</option>
3617 <option value="set">Set value(s)</option>
3618 </param>
3619 <when value="no_set">
3620 </when>
3621 <when value="set">
3622
3623 <param name="sample_counts_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3624 <param name="sample_counts_MOD_1_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
3625 </when>
3626 </conditional>
3627 <conditional name="CONDITIONAL_missing">
3628 <param name="CONDITIONAL_SELECT_missing" type="select" label="Set Missing" help="Generate sample- and variant-based missing data reports (or just one report if 'sample-only'/'variant-only' is specified). As of alpha 2, mixed MT hardcalls appear in the heterozygous haploid stats. Supported column sets in the sample-based report are: maybefid: FID, if that column was present in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was present in the input. sid: Force SID column to be written even when absent in the input. misspheno1: First active phenotype missing (Y/N)? Always 'Y' if no phenotypes are loaded. missphenos: A Y/N column for each loaded phenotype. (Can be combined with misspheno1 to force at least one such column.) nmissdosage: Number of missing dosages. nmiss: Number of missing hardcalls, not counting het haploids. nmisshh: Number of missing hardcalls, counting het haploids. hethap: Number of heterozygous haploid hardcalls. nobs: Denominator (male count on chrY, otherwise total sample count). fmissdosage: Missing dosage rate. fmiss: Missing hardcall rate, not counting het haploids. fmisshh: Missing hardcall rate, counting het haploids. The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss. Supported column sets in the variant-based report are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. nmissdosage: Number of missing dosages. nmiss: Number of missing hardcalls, not counting het haploids. nmisshh: Number of missing hardcalls, counting het haploids. hethap: Number of heterozygous haploid calls. nobs: Number of potentially valid calls. fmissdosage: Missing dosage rate. fmiss: Missing hardcall rate, not counting het haploids. fmisshh: Missing hardcall rate, counting het haploids. fhethap: Heterozygous haploid rate. The default is chrom,nmiss,nobs,fmiss." argument="--missing">
3629 <option value="no_set" selected="True">Don't set</option>
3630 <option value="set">Set value(s)</option>
3631 </param>
3632 <when value="no_set">
3633 </when>
3634 <when value="set">
3635
3636 <param name="missing_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3637 <conditional name="CONDITIONAL_missing_MOD_1">
3638 <param name="CONDITIONAL_SELECT_missing_MOD_1" type="select" label="How to set Missing">
3639 <option value="no_set" selected="True">Don't set</option>
3640 <option value="from_list">Select from list</option>
3641
3642 </param>
3643 <when value="no_set">
3644 </when>
3645
3646 <when value="from_list">
3647 <param name="missing_MOD_1" type="select" label="Select value">
3648 <option value="{sample-only">{sample-only</option>
3649 <option value="variant-only}">variant-only}</option>
3650 </param>
3651 </when>
3652 </conditional>
3653 <param name="missing_MOD_2_0" type="text" label="'scols='&lt;column set descriptor&gt;" value="" optional="False" argument="'scols='&lt;column set descriptor&gt;" help=""/>
3654 <param name="missing_MOD_3_0" type="text" label="'vcols='&lt;column set descriptor&gt;" value="" optional="False" argument="'vcols='&lt;column set descriptor&gt;" help=""/>
3655 </when>
3656 </conditional>
3657 <conditional name="CONDITIONAL_hardy">
3658 <param name="CONDITIONAL_SELECT_hardy" type="select" label="Set Hardy" help="Hardy-Weinberg exact test p-value report(s). * By default, only founders are considered; change this with --nonfounders. * chrX is now omitted from the main &lt;output prefix&gt;.hardy report. Instead, (if present) it gets its own &lt;output prefix&gt;.hardy.x report based on the method described in Graffelman J, Weir BS (2016) Hardy-Weinberg equilibrium and the X chromosome. * For variants with k alleles where k&gt;2, k separate 'biallelic' tests are performed, each reported on its own line. However, biallelic variants are normally reported on a single line, since the counts/frequencies would be mirror-images and the p-values would be the same. You can add the 'redundant' modifier to force biallelic variant results to be reported on two lines for parsing convenience. * There is currently no special handling of case/control phenotypes. Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. (A1 is always present, and positioned here.) ax: Non-A1 allele(s), comma-separated. gcounts: Hom-A1 count, total number of het-A1 calls, and total number of nonmissing calls with no copies of A1. On chrX, these are followed by male A1 and male non-A1 counts. gcount1col: gcounts values in a single comma-separated column. hetfreq: Observed and expected het-A1 frequencies. sexaf: Female and male A1 observed allele frequencies (chrX only). femalep: Female-only p/midp-value (chrX only). p: Hardy-Weinberg equilibrium exact test p/midp-value. The default is chrom,ax,gcounts,hetfreq,sexaf,p." argument="--hardy">
3659 <option value="no_set" selected="True">Don't set</option>
3660 <option value="set">Set value(s)</option>
3661 </param>
3662 <when value="no_set">
3663 </when>
3664 <when value="set">
3665
3666 <param name="hardy_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3667 <param name="hardy_MOD_1_0" type="text" label="'midp'" value="" optional="False" argument="'midp'" help=""/>
3668 <param name="hardy_MOD_2_0" type="text" label="'redundant'" value="" optional="False" argument="'redundant'" help=""/>
3669 <param name="hardy_MOD_3_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
3670 </when>
3671 </conditional>
3672 <conditional name="CONDITIONAL_indep_pairwise">
3673 <param name="CONDITIONAL_SELECT_indep_pairwise" type="select" label="Set Indep pairwise" help="Generate a list of variants in approximate linkage equilibrium. * For multiallelic variants, major allele counts are used in the r^2 computation. * With the 'kb' modifier, the window size is in kilobase instead of variant count units. (Pre-'kb' space is optional, i.e. &quot;--indep-pairwise 500 kb 0.5&quot; and &quot;--indep-pairwise 500kb 0.5&quot; have the same effect.) * The step size now defaults to 1 if it's unspecified, and *must* be 1 if the window is in kilobase units. * Note that you need to rerun PLINK using --extract or --exclude on the .prune.in/.prune.out file to apply the list to another computation... and as with other applications of --extract/--exclude, duplicate variant IDs are a problem. --indep-pairwise still runs to completion for now when duplicate variant IDs are present, but that will become an error in alpha 3." argument="--indep-pairwise">
3674 <option value="no_set" selected="True">Don't set</option>
3675 <option value="set">Set value(s)</option>
3676 </param>
3677 <when value="no_set">
3678 </when>
3679 <when value="set">
3680
3681 <param name="indep_pairwise_MOD_0_0" type="text" label="window size" value="" optional="True" argument="window size" help=""/>
3682 <param name="indep_pairwise_MOD_1_0" type="text" label="'kb'" value="" optional="False" argument="'kb'" help=""/>
3683 <param name="indep_pairwise_MOD_2_0" type="text" label="step size (variant ct)" value="" optional="False" argument="step size (variant ct)" help=""/>
3684 <param name="indep_pairwise_MOD_3_0" type="text" label="unphased-hardcall-r^2 threshold" value="" optional="True" argument="unphased-hardcall-r^2 threshold" help=""/>
3685 </when>
3686 </conditional>
3687 <conditional name="CONDITIONAL_ld">
3688 <param name="CONDITIONAL_SELECT_ld" type="select" label="Set Ld" help="This displays diplotype frequencies, r^2, and D' for a single pair of variants. * For multiallelic variants, major allele counts/dosages are used. * Phase information is used when both variants are on the same chromosome. * When there is at least one sample with unphased het calls for both variants, diplotype frequencies are estimated using the Hill equation. If there are multiple biologically possible local maxima, all are displayed, along with HWE exact test statistics. * By default, only hardcalls are considered. Add the 'dosage' modifier if you want dosages to be taken into account. (In the diploid case, an unphased dosage of x is interpreted as P(0/0) = 1 - x, P(0/1) = x when x is in 0..1.)" argument="--ld">
3689 <option value="no_set" selected="True">Don't set</option>
3690 <option value="set">Set value(s)</option>
3691 </param>
3692 <when value="no_set">
3693 </when>
3694 <when value="set">
3695
3696 <param name="ld_MOD_0_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/>
3697 <param name="ld_MOD_1_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/>
3698 <param name="ld_MOD_2_0" type="text" label="'dosage'" value="" optional="False" argument="'dosage'" help=""/>
3699 <param name="ld_MOD_3_0" type="text" label="'hwe-midp'" value="" optional="False" argument="'hwe-midp'" help=""/>
3700 </when>
3701 </conditional>
3702 <conditional name="CONDITIONAL_OVERLOADED_sample_diff">
3703 <param name="CONDITIONAL_OVERLOADED_SELECT_sample_diff" type="select" label="Choose argument form for Sample_diff" help="Overloaded argument, must chose a form">
3704 <option value="form_0">Form 0</option>
3705 <option value="form_1">Form 1</option>
3706 </param>
3707 <when value="form_0">
3708
3709 <conditional name="CONDITIONAL_sample_diff">
3710 <param name="CONDITIONAL_SELECT_sample_diff" type="select" label="Set Sample diff" help="" argument="--sample-diff">
3711 <option value="no_set" selected="True">Don't set</option>
3712 <option value="set">Set value(s)</option>
3713 </param>
3714 <when value="no_set">
3715 </when>
3716 <when value="set">
3717
3718 <param name="sample_diff_MOD_0_0" type="text" label="'id-delim='&lt;char&gt;" value="" optional="False" argument="'id-delim='&lt;char&gt;" help=""/>
3719 <conditional name="CONDITIONAL_sample_diff_MOD_1">
3720 <param name="CONDITIONAL_SELECT_sample_diff_MOD_1" type="select" label="How to set Sample diff">
3721 <option value="no_set" selected="True">Don't set</option>
3722 <option value="from_list">Select from list</option>
3723
3724 </param>
3725 <when value="no_set">
3726 </when>
3727
3728 <when value="from_list">
3729 <param name="sample_diff_MOD_1" type="select" label="Select value">
3730 <option value="'dosage'">'dosage'</option>
3731 <option value="'dosage='&lt;tolerance&gt;">'dosage='<tolerance></option>
3732 </param>
3733 </when>
3734 </conditional>
3735 <param name="sample_diff_MOD_2_0" type="text" label="'include-missing'" value="" optional="False" argument="'include-missing'" help=""/>
3736 <conditional name="CONDITIONAL_sample_diff_MOD_3">
3737 <param name="CONDITIONAL_SELECT_sample_diff_MOD_3" type="select" label="How to set Sample diff">
3738 <option value="no_set" selected="True">Don't set</option>
3739 <option value="from_list">Select from list</option>
3740
3741 </param>
3742 <when value="no_set">
3743 </when>
3744
3745 <when value="from_list">
3746 <param name="sample_diff_MOD_3" type="select" label="Select value">
3747 <option value="{pairwise">{pairwise</option>
3748 <option value="counts-only}">counts-only}</option>
3749 </param>
3750 </when>
3751 </conditional>
3752 <param name="sample_diff_MOD_4_0" type="text" label="'fname-id-delim='&lt;c&gt;" value="" optional="False" argument="'fname-id-delim='&lt;c&gt;" help=""/>
3753 <param name="sample_diff_MOD_5_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3754 <param name="sample_diff_MOD_6_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
3755 <param name="sample_diff_MOD_7_0" type="text" label="'counts-cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'counts-cols='&lt;column set descriptor&gt;" help=""/>
3756 <conditional name="CONDITIONAL_sample_diff_MOD_8">
3757 <param name="CONDITIONAL_SELECT_sample_diff_MOD_8" type="select" label="How to set Sample diff">
3758 <option value="no_set" selected="True">Don't set</option>
3759 <option value="from_list">Select from list</option>
3760
3761 </param>
3762 <when value="no_set">
3763 </when>
3764
3765 <when value="from_list">
3766 <param name="sample_diff_MOD_8" type="select" label="Select value">
3767 <option value="base=">base=</option>
3768 <option value="ids=">ids=</option>
3769 </param>
3770 </when>
3771 </conditional>
3772 <param name="sample_diff_MOD_9_0" type="text" label="sample ID" value="" optional="True" argument="sample ID" help=""/>
3773 <param name="sample_diff_MOD_10_0" type="text" label="other sample ID(s)..." value="" optional="False" argument="other sample ID(s)..." help="Multiple values are allowed"/>
3774 </when>
3775 </conditional>
3776 </when>
3777 <when value="form_1">
3778
3779 <conditional name="CONDITIONAL_sample_diff">
3780 <param name="CONDITIONAL_SELECT_sample_diff" type="select" label="Set Sample diff" help="(alias: --sdiff) Report discordances and discordance-counts between pairs of samples. If chrX or chrY is present, sex must be defined and consistent. * There are three ways to specify which sample pairs to compare. To compare a single baseline sample against some others, start the (space-delimited) sample ID list with 'base='. To perform an all-vs.-all comparison, start it with 'ids=' instead. To compare sample pairs listed in a file, use 'file='. Note that 'base='/'ids='/'file=' must be positioned after all modifiers. * Sample IDs are interpreted as if they were in a VCF header line, with 'id-delim=' having the usual effect. * By default, comparisons are based on hardcalls. Use 'dosage' to compare dosages instead; you can combine this with a tolerance in [0, 0.5). * By default, if one genotype is missing and the other isn't, that doesn't count as a difference; this can be changed with 'include-missing'. * By default, a single main report is written to &lt;output prefix&gt;[.&lt;base ID&gt;].sdiff. To write separate pairwise &lt;output prefix&gt;.&lt;ID1&gt;.&lt;ID2&gt;.sdiff reports for each compared ID pair, add the 'pairwise' modifier. To omit the main report, add the 'counts-only' modifier. (Note that, if you're only interested in nonmissing autosomal biallelic hardcalls, --make-king-table provides a more efficient way to compute just counts.) * By default, if an output filename has a multipart sample ID, the parts will be delimited by '_'; use 'fname-id-delim=' to change this. Supported main-report column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (Variant ID is always present, and positioned here.) ref: Reference allele. alt: All alternate alleles, comma-separated. maybefid: FID1/FID2, if that column was in the input. Requires 'id'. fid: Force FID1/FID2 even when FID was absent in the input. id: IID1/IID2. maybesid: SID1/SID2, if that column was in the input. Requires 'id'. sid: Force SID1/SID2 even when SID was absent in the input. geno: Unphased GT or DS for the two samples. The default is usually chrom,pos,ref,alt,maybefid,id,maybesid,geno; the sample IDs are removed from the default in 'pairwise' mode. Supported discordance-count-summary column sets are: maybefid: FID1/FID2, if that column was in the input. fid: Force FID1/FID2 even when FID was absent in the input. (IID1/IID2 are always present.) maybesid: SID1/SID2, if that column was in the input. sid: Force SID1/SID2 even when SID was absent in the input. nobs: Number of variants considered. This includes variants where one or both variants are missing iff 'include-missing' was specified. nobsibs: ibs0+ibs1+ibs2. ibs0: Number of diploid variants with no common hardcall alleles. ibs1: Number of diploid variants with exactly 1 common hardcall allele. ibs2: Number of diploid variants with both hardcall alleles matching. halfmiss: Number of variants with exactly 1 missing genotype/dosage. Ignored without 'include-missing'. diff: Total number of differences. The default is maybefid,maybesid,nobs,halfmiss,diff." argument="--sample-diff">
3781 <option value="no_set" selected="True">Don't set</option>
3782 <option value="set">Set value(s)</option>
3783 </param>
3784 <when value="no_set">
3785 </when>
3786 <when value="set">
3787
3788 <param name="sample_diff_MOD_0_0" type="text" label="'id-delim='&lt;char&gt;" value="" optional="False" argument="'id-delim='&lt;char&gt;" help=""/>
3789 <conditional name="CONDITIONAL_sample_diff_MOD_1">
3790 <param name="CONDITIONAL_SELECT_sample_diff_MOD_1" type="select" label="How to set Sample diff">
3791 <option value="no_set" selected="True">Don't set</option>
3792 <option value="from_list">Select from list</option>
3793
3794 </param>
3795 <when value="no_set">
3796 </when>
3797
3798 <when value="from_list">
3799 <param name="sample_diff_MOD_1" type="select" label="Select value">
3800 <option value="'dosage'">'dosage'</option>
3801 <option value="'dosage='&lt;tolerance&gt;">'dosage='<tolerance></option>
3802 </param>
3803 </when>
3804 </conditional>
3805 <param name="sample_diff_MOD_2_0" type="text" label="'include-missing'" value="" optional="False" argument="'include-missing'" help=""/>
3806 <conditional name="CONDITIONAL_sample_diff_MOD_3">
3807 <param name="CONDITIONAL_SELECT_sample_diff_MOD_3" type="select" label="How to set Sample diff">
3808 <option value="no_set" selected="True">Don't set</option>
3809 <option value="from_list">Select from list</option>
3810
3811 </param>
3812 <when value="no_set">
3813 </when>
3814
3815 <when value="from_list">
3816 <param name="sample_diff_MOD_3" type="select" label="Select value">
3817 <option value="{pairwise">{pairwise</option>
3818 <option value="counts-only}">counts-only}</option>
3819 </param>
3820 </when>
3821 </conditional>
3822 <param name="sample_diff_MOD_4_0" type="text" label="'fname-id-delim='&lt;c&gt;" value="" optional="False" argument="'fname-id-delim='&lt;c&gt;" help=""/>
3823 <param name="sample_diff_MOD_5_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3824 <param name="sample_diff_MOD_6_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
3825 <param name="sample_diff_MOD_7_0" type="text" label="'counts-cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'counts-cols='&lt;column set descriptor&gt;" help=""/>
3826 <param name="sample_diff_MOD_8_0" type="text" label="ID-pair file" value="" optional="True" argument="ID-pair file" help=""/>
3827 </when>
3828 </conditional>
3829 </when>
3830 </conditional>
3831 <conditional name="CONDITIONAL_make_king">
3832 <param name="CONDITIONAL_SELECT_make_king" type="select" label="Set Make king" help="KING-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in genome-wide association studies. By default, this writes a lower-triangular tab-delimited table of kinship coefficients to &lt;output prefix&gt;.king, and a list of the corresponding sample IDs to &lt;output prefix&gt;.king.id. The first row of the .king file contains a single &lt;genome 1-genome 2&gt; kinship coefficient, the second row has the &lt;genome 1-genome 3&gt; and &lt;genome 2-genome 3&gt; kinship values in that order, etc. * Only autosomes are currently considered. * Pedigree information is currently ignored; the between-family estimator is used for all pairs. * For multiallelic variants, REF allele counts are used. * If the 'square' or 'square0' modifier is present, a square matrix is written instead; 'square0' fills the upper right triangle with zeroes. * If the 'zs' modifier is present, the .king file is Zstd-compressed. * If the 'bin' modifier is present, a binary (square) matrix of double-precision floating point values, suitable for loading from R, is instead written to &lt;output prefix&gt;.king.bin. ('bin4' specifies single-precision numbers instead.) This can be combined with 'square0' if you still want the upper right zeroed out, or 'triangle' if you don't want to pad the upper right at all. * The computation can be subdivided with --parallel." argument="--make-king">
3833 <option value="no_set" selected="True">Don't set</option>
3834 <option value="set">Set value(s)</option>
3835 </param>
3836 <when value="no_set">
3837 </when>
3838 <when value="set">
3839
3840 <conditional name="CONDITIONAL_make_king_MOD_0">
3841 <param name="CONDITIONAL_SELECT_make_king_MOD_0" type="select" label="How to set Make king">
3842 <option value="no_set" selected="True">Don't set</option>
3843 <option value="from_list">Select from list</option>
3844
3845 </param>
3846 <when value="no_set">
3847 </when>
3848
3849 <when value="from_list">
3850 <param name="make_king_MOD_0" type="select" label="Select value">
3851 <option value="{square">{square</option>
3852 <option value="square0">square0</option>
3853 <option value="triangle}">triangle}</option>
3854 </param>
3855 </when>
3856 </conditional>
3857 <conditional name="CONDITIONAL_make_king_MOD_1">
3858 <param name="CONDITIONAL_SELECT_make_king_MOD_1" type="select" label="How to set Make king">
3859 <option value="no_set" selected="True">Don't set</option>
3860 <option value="from_list">Select from list</option>
3861
3862 </param>
3863 <when value="no_set">
3864 </when>
3865
3866 <when value="from_list">
3867 <param name="make_king_MOD_1" type="select" label="Select value">
3868 <option value="{zs">{zs</option>
3869 <option value="bin">bin</option>
3870 <option value="bin4}">bin4}</option>
3871 </param>
3872 </when>
3873 </conditional>
3874 </when>
3875 </conditional>
3876 <conditional name="CONDITIONAL_make_king_table">
3877 <param name="CONDITIONAL_SELECT_make_king_table" type="select" label="Set Make king table" help="Similar to --make-king, except results are reported in KING's original .kin0 text table format (with minor changes, e.g. row order is more friendly to incremental addition of samples), --king-table-filter can be used to restrict the report to high kinship values, and the 'rel-check' modifier can be used to restrict to same-FID pairs. Supported column sets are: maybefid: FID1/FID2, if that column was in the input. Requires 'id'. fid: Force FID1/FID2 even when FID was absent in the input. id: IID1/IID2 (column headers are actually 'ID1'/'ID2' to match KING). maybesid: SID1/SID2, if that column was in the input. Requires 'id'. sid: Force SID1/SID2 even when SID was absent in the input. nsnp: Number of variants considered (autosomal, neither call missing). hethet: Proportion/count of considered call pairs which are het-het. ibs0: Proportion/count of considered call pairs which are opposite homs. ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts. kinship: KING-robust between-family kinship estimator. The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship. hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is present. If id is omitted, a .kin0.id file is also written." argument="--make-king-table">
3878 <option value="no_set" selected="True">Don't set</option>
3879 <option value="set">Set value(s)</option>
3880 </param>
3881 <when value="no_set">
3882 </when>
3883 <when value="set">
3884
3885 <param name="make_king_table_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3886 <param name="make_king_table_MOD_1_0" type="text" label="'counts'" value="" optional="False" argument="'counts'" help=""/>
3887 <param name="make_king_table_MOD_2_0" type="text" label="'rel-check'" value="" optional="False" argument="'rel-check'" help=""/>
3888 <param name="make_king_table_MOD_3_0" type="text" label="'cols='&lt;col set descrip.&gt;" value="" optional="False" argument="'cols='&lt;col set descrip.&gt;" help=""/>
3889 </when>
3890 </conditional>
3891 <conditional name="CONDITIONAL_make_rel">
3892 <param name="CONDITIONAL_SELECT_make_rel" type="select" label="Set Make rel" help="Write a lower-triangular variance-standardized relationship matrix to &lt;output prefix&gt;.rel, and corresponding IDs to &lt;output prefix&gt;.rel.id. * This computation assumes that variants do not have very low MAF, or deviate greatly from Hardy-Weinberg equilibrium. * Also, it's usually best to perform this calculation on a variant set in approximate linkage equilibrium. * The 'cov' modifier replaces the variance-standardization step with basic mean-centering, causing a covariance matrix to be calculated instead. * The computation can be subdivided with --parallel." argument="--make-rel">
3893 <option value="no_set" selected="True">Don't set</option>
3894 <option value="set">Set value(s)</option>
3895 </param>
3896 <when value="no_set">
3897 </when>
3898 <when value="set">
3899
3900 <param name="make_rel_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/>
3901 <param name="make_rel_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/>
3902 <conditional name="CONDITIONAL_make_rel_MOD_2">
3903 <param name="CONDITIONAL_SELECT_make_rel_MOD_2" type="select" label="How to set Make rel">
3904 <option value="no_set" selected="True">Don't set</option>
3905 <option value="from_list">Select from list</option>
3906
3907 </param>
3908 <when value="no_set">
3909 </when>
3910
3911 <when value="from_list">
3912 <param name="make_rel_MOD_2" type="select" label="Select value">
3913 <option value="{square">{square</option>
3914 <option value="square0">square0</option>
3915 <option value="triangle}">triangle}</option>
3916 </param>
3917 </when>
3918 </conditional>
3919 <conditional name="CONDITIONAL_make_rel_MOD_3">
3920 <param name="CONDITIONAL_SELECT_make_rel_MOD_3" type="select" label="How to set Make rel">
3921 <option value="no_set" selected="True">Don't set</option>
3922 <option value="from_list">Select from list</option>
3923
3924 </param>
3925 <when value="no_set">
3926 </when>
3927
3928 <when value="from_list">
3929 <param name="make_rel_MOD_3" type="select" label="Select value">
3930 <option value="{zs">{zs</option>
3931 <option value="bin">bin</option>
3932 <option value="bin4}">bin4}</option>
3933 </param>
3934 </when>
3935 </conditional>
3936 </when>
3937 </conditional>
3938 <conditional name="CONDITIONAL_make_grm_list">
3939 <param name="CONDITIONAL_SELECT_make_grm_list" type="select" label="Set Make grm list" help="" argument="--make-grm-list">
3940 <option value="no_set" selected="True">Don't set</option>
3941 <option value="set">Set value(s)</option>
3942 </param>
3943 <when value="no_set">
3944 </when>
3945 <when value="set">
3946
3947 <param name="make_grm_list_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/>
3948 <param name="make_grm_list_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/>
3949 <param name="make_grm_list_MOD_2_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
3950 <conditional name="CONDITIONAL_make_grm_list_MOD_3">
3951 <param name="CONDITIONAL_SELECT_make_grm_list_MOD_3" type="select" label="How to set Make grm list">
3952 <option value="no_set" selected="True">Don't set</option>
3953 <option value="from_list">Select from list</option>
3954
3955 </param>
3956 <when value="no_set">
3957 </when>
3958
3959 <when value="from_list">
3960 <param name="make_grm_list_MOD_3" type="select" label="Select value">
3961 <option value="{id-header">{id-header</option>
3962 <option value="iid-only}">iid-only}</option>
3963 </param>
3964 </when>
3965 </conditional>
3966 </when>
3967 </conditional>
3968 <conditional name="CONDITIONAL_make_grm_bin">
3969 <param name="CONDITIONAL_SELECT_make_grm_bin" type="select" label="Set Make grm bin" help="--make-grm-list causes the relationships to be written to GCTA's original list format, which describes one pair per line, while --make-grm-bin writes them in GCTA 1.1+'s single-precision triangular binary format. Note that these formats explicitly report the number of valid observations (where neither sample has a missing call) for each pair, which is useful input for some scripts." argument="--make-grm-bin">
3970 <option value="no_set" selected="True">Don't set</option>
3971 <option value="set">Set value(s)</option>
3972 </param>
3973 <when value="no_set">
3974 </when>
3975 <when value="set">
3976
3977 <param name="make_grm_bin_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/>
3978 <param name="make_grm_bin_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/>
3979 <conditional name="CONDITIONAL_make_grm_bin_MOD_2">
3980 <param name="CONDITIONAL_SELECT_make_grm_bin_MOD_2" type="select" label="How to set Make grm bin">
3981 <option value="no_set" selected="True">Don't set</option>
3982 <option value="from_list">Select from list</option>
3983
3984 </param>
3985 <when value="no_set">
3986 </when>
3987
3988 <when value="from_list">
3989 <param name="make_grm_bin_MOD_2" type="select" label="Select value">
3990 <option value="{id-header">{id-header</option>
3991 <option value="iid-only}">iid-only}</option>
3992 </param>
3993 </when>
3994 </conditional>
3995 </when>
3996 </conditional>
3997 <conditional name="CONDITIONAL_OVERLOADED_pca">
3998 <param name="CONDITIONAL_OVERLOADED_SELECT_pca" type="select" label="Choose argument form for Pca" help="Overloaded argument, must chose a form">
3999 <option value="form_0">Form 0</option>
4000 <option value="form_1">Form 1</option>
4001 </param>
4002 <when value="form_0">
4003
4004 <conditional name="CONDITIONAL_pca">
4005 <param name="CONDITIONAL_SELECT_pca" type="select" label="Set Pca" help="" argument="--pca">
4006 <option value="no_set" selected="True">Don't set</option>
4007 <option value="set">Set value(s)</option>
4008 </param>
4009 <when value="no_set">
4010 </when>
4011 <when value="set">
4012
4013 <param name="pca_MOD_0_0" type="text" label="count" value="" optional="False" argument="count" help=""/>
4014 <conditional name="CONDITIONAL_pca_MOD_1">
4015 <param name="CONDITIONAL_SELECT_pca_MOD_1" type="select" label="How to set Pca">
4016 <option value="no_set" selected="True">Don't set</option>
4017 <option value="from_list">Select from list</option>
4018
4019 </param>
4020 <when value="no_set">
4021 </when>
4022
4023 <when value="from_list">
4024 <param name="pca_MOD_1" type="select" label="Select value">
4025 <option value="{approx">{approx</option>
4026 <option value="meanimpute}">meanimpute}</option>
4027 </param>
4028 </when>
4029 </conditional>
4030 <param name="pca_MOD_2_0" type="text" label="'scols='&lt;col set descriptor&gt;" value="" optional="False" argument="'scols='&lt;col set descriptor&gt;" help=""/>
4031 </when>
4032 </conditional>
4033 </when>
4034 <when value="form_1">
4035
4036 <conditional name="CONDITIONAL_pca">
4037 <param name="CONDITIONAL_SELECT_pca" type="select" label="Set Pca" help="['scols='&lt;col set descriptor&gt;] ['vcols='&lt;col set descriptor&gt;] Extracts top principal components from the variance-standardized relationship matrix. * It is usually best to perform this calculation on a variant set in approximate linkage equilibrium, with no very-low-MAF variants. * By default, 10 PCs are extracted; you can adjust this by passing a numeric parameter. (Note that 10 is lower than the PLINK 1.9 default of 20; this is due to the randomized algorithm's memory footprint growing quadratically w.r.t. the PC count.) * The 'approx' modifier causes the standard deterministic computation to be replaced with the randomized algorithm originally implemented for Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ, Price AL (2016) Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. This can be a good idea when you have &gt;5k samples. * The randomized algorithm always uses mean imputation for missing genotype calls. For comparison purposes, you can use the 'meanimpute' modifier to request this behavior for the standard computation. * 'scols=' can be used to customize how sample IDs appear in the .eigenvec file. (maybefid, fid, maybesid, and sid supported; default is maybefid,maybesid.) * The 'biallelic-var-wts' modifier requests an additional one-line-per-variant .eigenvec.var file with PCs expressed as variant weights instead of sample weights, with the condition that all variants must be biallelic. When it's present, 'vzs' causes the .eigenvec.var file to be Zstd-compressed. 'vcols=' can be used to customize the report columns; supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. maj: Major allele. nonmaj: All nonmajor alleles, comma-separated. (PCs are always present, and positioned here. Signs are w.r.t. the major, not necessarily reference, allele.) Default is chrom,maj,nonmaj. * In this build, 'var-wts' generates the same report as biallelic-var-wts, except with the &quot;all variants must be biallelic&quot; restriction lifted. This is temporary. It will no longer be supported as of alpha 3; instead, there will be an 'allele-wts' mode which seamlessly handles multiallelic variants, at the cost of generating more verbose one-line-per-allele output." argument="--pca">
4038 <option value="no_set" selected="True">Don't set</option>
4039 <option value="set">Set value(s)</option>
4040 </param>
4041 <when value="no_set">
4042 </when>
4043 <when value="set">
4044
4045 <conditional name="CONDITIONAL_pca_MOD_0">
4046 <param name="CONDITIONAL_SELECT_pca_MOD_0" type="select" label="How to set Pca">
4047 <option value="no_set" selected="True">Don't set</option>
4048 <option value="from_list">Select from list</option>
4049
4050 </param>
4051 <when value="no_set">
4052 </when>
4053
4054 <when value="from_list">
4055 <param name="pca_MOD_0" type="select" label="Select value">
4056 <option value="{biallelic-var-wts">{biallelic-var-wts</option>
4057 <option value="var-wts}">var-wts}</option>
4058 </param>
4059 </when>
4060 </conditional>
4061 <param name="pca_MOD_1_0" type="text" label="count" value="" optional="False" argument="count" help=""/>
4062 <conditional name="CONDITIONAL_pca_MOD_2">
4063 <param name="CONDITIONAL_SELECT_pca_MOD_2" type="select" label="How to set Pca">
4064 <option value="no_set" selected="True">Don't set</option>
4065 <option value="from_list">Select from list</option>
4066
4067 </param>
4068 <when value="no_set">
4069 </when>
4070
4071 <when value="from_list">
4072 <param name="pca_MOD_2" type="select" label="Select value">
4073 <option value="{approx">{approx</option>
4074 <option value="meanimpute}">meanimpute}</option>
4075 </param>
4076 </when>
4077 </conditional>
4078 <param name="pca_MOD_3_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
4079 </when>
4080 </conditional>
4081 </when>
4082 </conditional>
4083 <conditional name="CONDITIONAL_king_cutoff">
4084 <param name="CONDITIONAL_SELECT_king_cutoff" type="select" label="Set King cutoff" help="Exclude one member of each pair of samples with KING-robust kinship greater than the given threshold. Remaining/excluded sample IDs are written to &lt;output prefix&gt;.king.cutoff.in.id + .king.cutoff.out.id. If present, the .king.bin file must be triangular (either precision is ok)." argument="--king-cutoff">
4085 <option value="no_set" selected="True">Don't set</option>
4086 <option value="set">Set value(s)</option>
4087 </param>
4088 <when value="no_set">
4089 </when>
4090 <when value="set">
4091
4092 <param name="king_cutoff_MOD_0_0" type="text" label=".king.bin + .king.id fileset prefix" value="" optional="False" argument=".king.bin + .king.id fileset prefix" help=""/>
4093 <param name="king_cutoff_MOD_1_0" type="text" label="threshold" value="" optional="True" argument="threshold" help=""/>
4094 </when>
4095 </conditional>
4096 <conditional name="CONDITIONAL_write_covar">
4097 <param name="CONDITIONAL_SELECT_write_covar" type="select" label="Set Write covar" help="If covariates are defined, an updated version (with all filters applied) is automatically written to &lt;output prefix&gt;.cov whenever --make-pgen, --make-just-psam, --export, or a similar command is present. However, if you do not wish to simultaneously generate a new sample file, you can use --write-covar to just produce a pruned covariate file. Supported column sets are: maybefid: FID, if that column was in the input. fid: Force FID column to be written even when absent in the input. maybesid: SID, if that column was in the input. sid: Force SID column to be written even when absent in the input. maybeparents: Father/mother IIDs ('0' = missing), if columns in input. parents: Force PAT/MAT columns to be written even when absent in input. sex: '1' = male, '2' = female, 'NA' = missing. pheno1: First active phenotype. If none, all column entries are set to the --output-missing-phenotype string. phenos: All active phenotypes, if any. (Can be combined with pheno1 to force at least one phenotype column to be written.) (Covariates are always present, and positioned here.) The default is maybefid,maybesid." argument="--write-covar">
4098 <option value="no_set" selected="True">Don't set</option>
4099 <option value="set">Set value(s)</option>
4100 </param>
4101 <when value="no_set">
4102 </when>
4103 <when value="set">
4104
4105 <param name="write_covar_MOD_0_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
4106 </when>
4107 </conditional>
4108 <param name="write_samples" type="boolean" label="Write samples" truevalue="--write-samples" falsevalue="" optional="true" argument="--write-samples" help="Report IDs of all samples which pass your filters/inclusion thresholds." checked="False"/>
4109 <conditional name="CONDITIONAL_write_snplist">
4110 <param name="CONDITIONAL_SELECT_write_snplist" type="select" label="Set Write snplist" help="List all variants which pass your filters/inclusion thresholds." argument="--write-snplist">
4111 <option value="no_set" selected="True">Don't set</option>
4112 <option value="set">Set value(s)</option>
4113 </param>
4114 <when value="no_set">
4115 </when>
4116 <when value="set">
4117
4118 <param name="write_snplist_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
4119 </when>
4120 </conditional>
4121 <conditional name="CONDITIONAL_glm">
4122 <param name="CONDITIONAL_SELECT_glm" type="select" label="Set Glm" help="[{genotypic | hethom | dominant | recessive}] ['interaction'] ['hide-covar'] ['intercept'] [{no-firth | firth-fallback | firth}] ['cols='&lt;col set desc.&gt;] ['local-covar='&lt;file&gt;] ['local-pvar='&lt;file&gt;] ['local-psam='&lt;file&gt;] ['local-omit-last' | 'local-cats='&lt;category ct&gt;] Basic association analysis on quantitative and/or case/control phenotypes. For each variant, a linear (for quantitative traits) or logistic (for case/control) regression is run with the phenotype as the dependent variable, and nonmajor allele dosage(s) and a constant-1 column as predictors. * There is usually an additive effect line for every nonmajor allele, and no such line for the major allele. To omit REF alleles instead of major alleles, add the 'omit-ref' modifier. (When performing interaction testing, this tends to cause the multicollinearity check to fail for low-ref-frequency variants.) * By default, sex (male = 1, female = 2; note that this is a change from PLINK 1.x) is automatically added as a predictor for X chromosome variants, and no others. The 'sex' modifier causes it to be added everywhere (except chrY), while 'no-x-sex' excludes it entirely. * The 'log10' modifier causes p-values to be reported in -log10(p) form. * 'pheno-ids' causes the samples used in each set of regressions to be written to an .id file. (When the samples differ on chrX or chrY, .x.id and/or .y.id files are also written.) * The 'genotypic' modifier adds an additive effect/dominance deviation 2df joint test (0-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and 0..1..0 coding instead. * 'dominant' and 'recessive' specify a model assuming full dominance or recessiveness, respectively, for the ref allele. I.e. the genotype column is recoded as 0..1..1 or 0..0..1, respectively. * 'interaction' adds genotype x covariate interactions to the model. Note that this tends to produce 'NA' results (due to the multicollinearity check) when the reference allele is 'wrong'; --maj-ref can be used to enable analysis of those variants. * Additional predictors can be added with --covar. By default, association statistics are reported for all nonconstant predictors; 'hide-covar' suppresses covariate-only results, while 'intercept' causes intercepts to be reported. * For logistic regression, when the phenotype [quasi-]separates the genotype, an NA result is currently reported by default. To fall back on Firth logistic regression instead when the basic logistic regression fails to converge, add the 'firth-fallback' modifier (highly recommended, will become the default when beta testing begins). To eliminate the special case and use Firth logistic regression everywhere, add 'firth'. 'no-firth' can be used to prevent Firth regression from being attempted in a way that'll still work after alpha testing completes. * To add covariates which are not constant across all variants, add the 'local-covar=', 'local-pvar=', and 'local-psam=' modifiers, and use full filenames for each. Normally, the local-covar file should have c * n real-valued columns, where the first c columns correspond to the first sample in the local-psam file, columns (c+1) to 2c correspond to the second sample, etc.; and the mth line corresponds to the mth nonheader line of the local-pvar file. (Variants outside of the local-pvar file are excluded from the regression.) The local covariates are assigned the names LOCAL1, LOCAL2, etc.; to exclude the last local covariate from the regression (necessary if they are e.g. local ancestry coefficients which sum to 1), add 'local-omit-last'. Alternatively, with 'local-cats='&lt;k&gt;, the local-covar file is expected to have n columns with integer-valued entries in [1, k]. These category assignments are expanded into (k-1) local covariates in the usual manner. The main report supports the following column sets: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. (A1 is always present, and positioned here. For multiallelic variants, this column may contain multiple comma-separated alleles when the result doesn't depend on which allele is A1.) ax: Non-A1 alleles, comma-separated. a1count: A1 allele count (can be decimal with dosage data). totallele: Allele observation count (can be higher than --freq value, due to inclusion of het haploids and chrX model). a1countcc: A1 count in cases, then controls (case/control only). totallelecc: Case and control allele observation counts. gcountcc: Genotype hardcall counts (neither-A1, het-A1, A1-A1) in cases, then controls (case/control only). a1freq: A1 allele frequency. a1freqcc: A1 frequency in cases, then controls (case/control only). machr2: Unphased MaCH imputation quality (frequently labeled 'INFO'). firth: Reports whether Firth regression was used (firth-fallback only). test: Test identifier. (Required unless only one test is run.) nobs: Number of samples in the regression. beta: Regression coefficient (for A1 if additive test). orbeta: Odds ratio for case/control, beta for quantitative traits. (Ignored if 'beta' column set included.) se: Standard error of beta. ci: Bounds of symmetric approximate confidence interval (requires --ci). tz: T-statistic for linear regression, Wald Z-score for logistic/Firth. p: Asymptotic p-value (or -log10(p)) for T/Z-statistic. err: Error code for NA results. The default is chrom,pos,ref,alt,firth,test,nobs,orbeta,se,ci,tz,p." argument="--glm">
4123 <option value="no_set" selected="True">Don't set</option>
4124 <option value="set">Set value(s)</option>
4125 </param>
4126 <when value="no_set">
4127 </when>
4128 <when value="set">
4129
4130 <param name="glm_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
4131 <param name="glm_MOD_1_0" type="text" label="'omit-ref'" value="" optional="False" argument="'omit-ref'" help=""/>
4132 <conditional name="CONDITIONAL_glm_MOD_2">
4133 <param name="CONDITIONAL_SELECT_glm_MOD_2" type="select" label="How to set Glm">
4134 <option value="no_set" selected="True">Don't set</option>
4135 <option value="from_list">Select from list</option>
4136
4137 </param>
4138 <when value="no_set">
4139 </when>
4140
4141 <when value="from_list">
4142 <param name="glm_MOD_2" type="select" label="Select value">
4143 <option value="{sex">{sex</option>
4144 <option value="no-x-sex}">no-x-sex}</option>
4145 </param>
4146 </when>
4147 </conditional>
4148 <param name="glm_MOD_3_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/>
4149 <param name="glm_MOD_4_0" type="text" label="'pheno-ids'" value="" optional="False" argument="'pheno-ids'" help=""/>
4150 </when>
4151 </conditional>
4152 <conditional name="CONDITIONAL_score">
4153 <param name="CONDITIONAL_SELECT_score" type="select" label="Set Score" help="Apply linear scoring system(s) to each sample. The input file should have one line per scored variant. Variant IDs are read from column #i and allele codes are read from column #j, where i defaults to 1 and j defaults to i+1. For now, only one allele per multiallelic variant may be assigned an explicit score; contact us if you need this changed. * By default, a single column of input coefficients is read from column #k, where k defaults to j+1. (--score-col-nums can be used to specify multiple columns.) * 'header-read' causes the first line of the input file to be treated as a header line containing score names. Otherwise, score(s) are assigned the names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line to be entirely ignored. * By default, copies of unnamed alleles contribute zero to score, while missing genotypes contribute an amount proportional to the loaded (via --read-freq) or imputed allele frequency. To throw out missing observations instead (decreasing the denominator in the final average when this happens), use the 'no-mean-imputation' modifier. * You can use the 'center' modifier to shift all genotypes to mean zero, or 'variance-standardize' to linearly transform the genotypes to mean-0, variance-1. * The 'dominant' modifier causes dosages greater than 1 to be treated as 1, while 'recessive' uses max(dosage - 1, 0) on diploid chromosomes. ('dominant', 'recessive', and 'variance-standardize' cannot be used with chrX.) * The 'se' modifier causes the input coefficients to be treated as independent standard errors; in this case, standard errors for the score average/sum are reported. (Note that this will systematically underestimate standard errors when scored variants are in LD.) * By default, --score errors out if a variant ID in the input file appears multiple times in the main dataset. Use the 'ignore-dup-ids' modifier to skip them instead (a warning is still printed if such variants are present). * The 'list-variants[-zs]' modifier causes variant IDs used for scoring to be written to &lt;output prefix&gt;.sscore.vars[.zst]. The main report supports the following column sets: maybefid: FID, if that column was in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was in the input. sid: Force SID column to be written even when absent in the input. pheno1: First active phenotype. phenos: All active phenotypes, if any. nmissallele: Number of nonmissing alleles. denom: Denominator of score average (equal to nmissallele value when 'no-mean-imputation' specified). dosagesum: Sum of named allele dosages. scoreavgs: Score averages. scoresums: Score sums. The default is maybefid,maybesid,phenos,nmissallele,dosagesum,scoreavgs. For more sophisticated polygenic risk scoring, we recommend the PRSice-2 software package (https://www.prsice.info/ )." argument="--score">
4154 <option value="no_set" selected="True">Don't set</option>
4155 <option value="set">Set value(s)</option>
4156 </param>
4157 <when value="no_set">
4158 </when>
4159 <when value="set">
4160
4161 <param name="score_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
4162 <param name="score_MOD_1_0" type="text" label="i" value="" optional="False" argument="i" help=""/>
4163 <param name="score_MOD_2_0" type="text" label="j" value="" optional="False" argument="j" help=""/>
4164 <param name="score_MOD_3_0" type="text" label="k" value="" optional="False" argument="k" help=""/>
4165 <conditional name="CONDITIONAL_score_MOD_4">
4166 <param name="CONDITIONAL_SELECT_score_MOD_4" type="select" label="How to set Score">
4167 <option value="no_set" selected="True">Don't set</option>
4168 <option value="from_list">Select from list</option>
4169
4170 </param>
4171 <when value="no_set">
4172 </when>
4173
4174 <when value="from_list">
4175 <param name="score_MOD_4" type="select" label="Select value">
4176 <option value="{header">{header</option>
4177 <option value="header-read}">header-read}</option>
4178 </param>
4179 </when>
4180 </conditional>
4181 <conditional name="CONDITIONAL_score_MOD_5">
4182 <param name="CONDITIONAL_SELECT_score_MOD_5" type="select" label="How to set Score">
4183 <option value="no_set" selected="True">Don't set</option>
4184 <option value="from_list">Select from list</option>
4185
4186 </param>
4187 <when value="no_set">
4188 </when>
4189
4190 <when value="from_list">
4191 <param name="score_MOD_5" type="select" label="Select value">
4192 <option value="{center">{center</option>
4193 <option value="variance-standardize">variance-standardize</option>
4194 <option value="dominant">dominant</option>
4195 <option value="recessive}">recessive}</option>
4196 </param>
4197 </when>
4198 </conditional>
4199 <param name="score_MOD_6_0" type="text" label="'no-mean-imputation'" value="" optional="False" argument="'no-mean-imputation'" help=""/>
4200 <param name="score_MOD_7_0" type="text" label="'se'" value="" optional="False" argument="'se'" help=""/>
4201 <param name="score_MOD_8_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
4202 <param name="score_MOD_9_0" type="text" label="'ignore-dup-ids'" value="" optional="False" argument="'ignore-dup-ids'" help=""/>
4203 <conditional name="CONDITIONAL_score_MOD_10">
4204 <param name="CONDITIONAL_SELECT_score_MOD_10" type="select" label="How to set Score">
4205 <option value="no_set" selected="True">Don't set</option>
4206 <option value="from_list">Select from list</option>
4207
4208 </param>
4209 <when value="no_set">
4210 </when>
4211
4212 <when value="from_list">
4213 <param name="score_MOD_10" type="select" label="Select value">
4214 <option value="{list-variants">{list-variants</option>
4215 <option value="list-variants-zs}">list-variants-zs}</option>
4216 </param>
4217 </when>
4218 </conditional>
4219 <param name="score_MOD_11_0" type="text" label="'cols='&lt;col set descriptor&gt;" value="" optional="False" argument="'cols='&lt;col set descriptor&gt;" help=""/>
4220 </when>
4221 </conditional>
4222 <conditional name="CONDITIONAL_variant_score">
4223 <param name="CONDITIONAL_SELECT_variant_score" type="select" label="Set Variant score" help="(alias: --vscore) Apply linear scoring system(s) to each variant. Each reported variant score is the dot product of a sample-weight vector with the total-ALT-dosage vector, with MAF-based mean imputation applied to missing dosages. Input file format: one line per sample, each starting with an ID and followed by scoring weight(s); it can also have a header line with the sample ID representation and the score name(s). The usual .vscore text report supports the following column sets: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. altfreq: ALT allele frequency used for mean-imputation. nmiss: Number of missing (and thus mean-imputed) dosages. nobs: Number of (nonmissing) sample observations. (Variant scores are always present, and positioned here.) Default is chrom,pos,ref,alt. If binary output is requested instead, the main .vscore.bin matrix contains double-precision floating-point values, column (score) ID(s) are saved to a &lt;output prefix&gt;.vscore.cols, and variant IDs are saved to &lt;output prefix&gt;.vscore.vars[.zst]." argument="--variant-score">
4224 <option value="no_set" selected="True">Don't set</option>
4225 <option value="set">Set value(s)</option>
4226 </param>
4227 <when value="no_set">
4228 </when>
4229 <when value="set">
4230
4231 <param name="variant_score_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
4232 <param name="variant_score_MOD_1_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
4233 <conditional name="CONDITIONAL_variant_score_MOD_2">
4234 <param name="CONDITIONAL_SELECT_variant_score_MOD_2" type="select" label="How to set Variant score">
4235 <option value="no_set" selected="True">Don't set</option>
4236 <option value="from_list">Select from list</option>
4237
4238 </param>
4239 <when value="no_set">
4240 </when>
4241
4242 <when value="from_list">
4243 <param name="variant_score_MOD_2" type="select" label="Select value">
4244 <option value="'bin'">'bin'</option>
4245 <option value="'cols='&lt;col set descriptor&gt;">'cols='<col set descriptor></option>
4246 </param>
4247 </when>
4248 </conditional>
4249 </when>
4250 </conditional>
4251 <conditional name="CONDITIONAL_adjust_file">
4252 <param name="CONDITIONAL_SELECT_adjust_file" type="select" label="Set Adjust file" help="Given a file with unfiltered association test results, report some basic multiple-testing corrections, sorted in increasing-p-value order. * 'gc' causes genomic-controlled p-values to be used in the formulas. (This tends to be overly conservative. We note that LD Score regression usually does a better job of calibrating lambda; see Lee JJ, McGue M, Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an estimator of confounding and genetic correlations in genome-wide association studies.) * 'log10' causes negative base 10 logs of p-values to be reported, instead of raw p-values. 'input-log10' specifies that the input file contains -log10(p) values. * If the input file contains multiple tests per variant which are distinguished by a 'TEST' column (true for --linear/--logistic/--glm), you must use 'test=' to select the test to process. The following column sets are supported: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. a1: Tested allele. (Omitted if missing from input file.) unadj: Unadjusted p-value. gc: Devlin &amp; Roeder (1999) genomic control corrected p-value (additive models only). qq: P-value quantile. bonf: Bonferroni correction. holm: Holm-Bonferroni (1979) adjusted p-value. sidakss: Sidak single-step adjusted p-value. sidaksd: Sidak step-down adjusted p-value. fdrbh: Benjamini &amp; Hochberg (1995) step-up false discovery control. fdrby: Benjamini &amp; Yekutieli (2001) step-up false discovery control. Default set is chrom,a1,unadj,gc,bonf,holm,sidakss,sidaksd,fdrbh,fdrby." argument="--adjust-file">
4253 <option value="no_set" selected="True">Don't set</option>
4254 <option value="set">Set value(s)</option>
4255 </param>
4256 <when value="no_set">
4257 </when>
4258 <when value="set">
4259
4260 <param name="adjust_file_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
4261 <param name="adjust_file_MOD_1_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
4262 <param name="adjust_file_MOD_2_0" type="text" label="'gc'" value="" optional="False" argument="'gc'" help=""/>
4263 <param name="adjust_file_MOD_3_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
4264 <param name="adjust_file_MOD_4_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/>
4265 <param name="adjust_file_MOD_5_0" type="text" label="'input-log10'" value="" optional="False" argument="'input-log10'" help=""/>
4266 <param name="adjust_file_MOD_6_0" type="text" label="'test='&lt;test name, case-sensitive&gt;" value="" optional="False" argument="'test='&lt;test name, case-sensitive&gt;" help=""/>
4267 </when>
4268 </conditional>
4269 <conditional name="CONDITIONAL_genotyping_rate">
4270 <param name="CONDITIONAL_SELECT_genotyping_rate" type="select" label="Set Genotyping rate" help="Report genotyping rate in log (this was automatic in PLINK 1.x)." argument="--genotyping-rate">
4271 <option value="no_set" selected="True">Don't set</option>
4272 <option value="set">Set value(s)</option>
4273 </param>
4274 <when value="no_set">
4275 </when>
4276 <when value="set">
4277
4278 <param name="genotyping_rate_MOD_0_0" type="text" label="'dosage'" value="" optional="False" argument="'dosage'" help=""/>
4279 </when>
4280 </conditional>
4281 <param name="pgen_info" type="boolean" label="Pgen info" truevalue="--pgen-info" falsevalue="" optional="true" argument="--pgen-info" help="Reports basic information about a .pgen file." checked="False"/>
4282 <param name="validate" type="boolean" label="Validate" truevalue="--validate" falsevalue="" optional="true" argument="--validate" help="Validates all variant records in a .pgen file." checked="False"/>
4283 <conditional name="CONDITIONAL_zst_decompress">
4284 <param name="CONDITIONAL_SELECT_zst_decompress" type="select" label="Set Zst decompress" help="(alias: --zd) Decompress a Zstd-compressed file. If no output filename is specified, the file is decompressed to standard output. This cannot be used with any other flags, and does not cause a log file to be generated." argument="--zst-decompress">
4285 <option value="no_set" selected="True">Don't set</option>
4286 <option value="set">Set value(s)</option>
4287 </param>
4288 <when value="no_set">
4289 </when>
4290 <when value="set">
4291
4292 <param name="zst_decompress_MOD_0_0" type="text" label=".zst file" value="" optional="True" argument=".zst file" help=""/>
4293 <param name="zst_decompress_MOD_1_0" type="text" label="output filename" value="" optional="False" argument="output filename" help=""/>
4294 </when>
4295 </conditional>
4296 <conditional name="CONDITIONAL_silent">
4297 <param name="CONDITIONAL_SELECT_silent" type="select" label="Set Silent" help="Suppress regular output to console. (Error-output is not suppressed.) " argument="--silent">
4298 <option value="no_set" selected="True">Don't set</option>
4299 <option value="set">Set value(s)</option>
4300 </param>
4301 <when value="no_set">
4302 </when>
4303 <when value="set">
4304
4305 </when>
4306 </conditional>
4307 <conditional name="CONDITIONAL_double_id">
4308 <param name="CONDITIONAL_SELECT_double_id" type="select" label="Set Double id" help="Set both FIDs and IIDs to the VCF/.bgen sample ID. " argument="--double-id">
4309 <option value="no_set" selected="True">Don't set</option>
4310 <option value="set">Set value(s)</option>
4311 </param>
4312 <when value="no_set">
4313 </when>
4314 <when value="set">
4315
4316 </when>
4317 </conditional>
4318 <conditional name="CONDITIONAL_const_fid">
4319 <param name="CONDITIONAL_SELECT_const_fid" type="select" label="Set Const fid" help="Set all FIDs to the given constant. If '0' (the default), no FID column is created. " argument="--const-fid">
4320 <option value="no_set" selected="True">Don't set</option>
4321 <option value="set">Set value(s)</option>
4322 </param>
4323 <when value="no_set">
4324 </when>
4325 <when value="set">
4326
4327 <param name="const_fid_MOD_0_0" type="text" label="ID" value="" optional="False" argument="ID" help=""/>
4328 </when>
4329 </conditional>
4330 <conditional name="CONDITIONAL_id_delim">
4331 <param name="CONDITIONAL_SELECT_id_delim" type="select" label="Set Id delim" help="Normally parses single-delimiter sample IDs as &lt;FID&gt;&lt;d&gt;&lt;IID&gt;, and double-delimiter IDs as &lt;FID&gt;&lt;d&gt;&lt;IID&gt;&lt;d&gt;&lt;SID&gt;; default delimiter is '_'. --id-delim can no longer be used with --double-id/--const-fid; it will error out if any ID lacks the delimiter. " argument="--id-delim">
4332 <option value="no_set" selected="True">Don't set</option>
4333 <option value="set">Set value(s)</option>
4334 </param>
4335 <when value="no_set">
4336 </when>
4337 <when value="set">
4338
4339 <param name="id_delim_MOD_0_0" type="text" label="d" value="" optional="False" argument="d" help=""/>
4340 </when>
4341 </conditional>
4342 <conditional name="CONDITIONAL_idspace_to">
4343 <param name="CONDITIONAL_SELECT_idspace_to" type="select" label="Set Idspace to" help="Convert spaces in VCF/.bgen sample IDs to the given character. " argument="--idspace-to">
4344 <option value="no_set" selected="True">Don't set</option>
4345 <option value="set">Set value(s)</option>
4346 </param>
4347 <when value="no_set">
4348 </when>
4349 <when value="set">
4350
4351 <param name="idspace_to_MOD_0_0" type="text" label="c" value="" optional="True" argument="c" help=""/>
4352 </when>
4353 </conditional>
4354 <conditional name="CONDITIONAL_iid_sid">
4355 <param name="CONDITIONAL_SELECT_iid_sid" type="select" label="Set Iid sid" help="Make --id-delim and --sample-diff interpret two-token sample IDs as IID-SID instead of FID-IID. " argument="--iid-sid">
4356 <option value="no_set" selected="True">Don't set</option>
4357 <option value="set">Set value(s)</option>
4358 </param>
4359 <when value="no_set">
4360 </when>
4361 <when value="set">
4362
4363 </when>
4364 </conditional>
4365 <conditional name="CONDITIONAL_vcf_require_gt">
4366 <param name="CONDITIONAL_SELECT_vcf_require_gt" type="select" label="Set Vcf require gt" help="Skip variants with no GT field. " argument="--vcf-require-gt">
4367 <option value="no_set" selected="True">Don't set</option>
4368 <option value="set">Set value(s)</option>
4369 </param>
4370 <when value="no_set">
4371 </when>
4372 <when value="set">
4373
4374 </when>
4375 </conditional>
4376 <conditional name="CONDITIONAL_vcf_min_gq">
4377 <param name="CONDITIONAL_SELECT_vcf_min_gq" type="select" label="Set Vcf min gq" help="No-call genotypes when GQ is present and below the threshold. " argument="--vcf-min-gq">
4378 <option value="no_set" selected="True">Don't set</option>
4379 <option value="set">Set value(s)</option>
4380 </param>
4381 <when value="no_set">
4382 </when>
4383 <when value="set">
4384
4385 <param name="vcf_min_gq_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4386 </when>
4387 </conditional>
4388 <conditional name="CONDITIONAL_vcf_max_dp">
4389 <param name="CONDITIONAL_SELECT_vcf_max_dp" type="select" label="Set Vcf max dp" help="No-call genotypes when DP is present and above/below " argument="--vcf-max-dp">
4390 <option value="no_set" selected="True">Don't set</option>
4391 <option value="set">Set value(s)</option>
4392 </param>
4393 <when value="no_set">
4394 </when>
4395 <when value="set">
4396
4397 <param name="vcf_max_dp_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4398 </when>
4399 </conditional>
4400 <conditional name="CONDITIONAL_vcf_min_dp">
4401 <param name="CONDITIONAL_SELECT_vcf_min_dp" type="select" label="Set Vcf min dp" help="" argument="--vcf-min-dp">
4402 <option value="no_set" selected="True">Don't set</option>
4403 <option value="set">Set value(s)</option>
4404 </param>
4405 <when value="no_set">
4406 </when>
4407 <when value="set">
4408
4409 <param name="vcf_min_dp_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4410 </when>
4411 </conditional>
4412 <conditional name="CONDITIONAL_vcf_half_call">
4413 <param name="CONDITIONAL_SELECT_vcf_half_call" type="select" label="Set Vcf half call" help="Specify how '0/.' and similar VCF GT values should be handled. The following four modes are supported: * 'error'/'e' (default) errors out and reports line #. * 'haploid'/'h' treats them as haploid calls. * 'missing'/'m' treats them as missing. * 'reference'/'r' treats the missing value as 0. " argument="--vcf-half-call">
4414 <option value="no_set" selected="True">Don't set</option>
4415 <option value="set">Set value(s)</option>
4416 </param>
4417 <when value="no_set">
4418 </when>
4419 <when value="set">
4420
4421 <param name="vcf_half_call_MOD_0_0" type="text" label="m" value="" optional="True" argument="m" help=""/>
4422 </when>
4423 </conditional>
4424 <conditional name="CONDITIONAL_oxford_single_chr">
4425 <param name="CONDITIONAL_SELECT_oxford_single_chr" type="select" label="Set Oxford single chr" help="Specify single-chromosome .gen/.bgen file with no useful chromosome info inside. " argument="--oxford-single-chr">
4426 <option value="no_set" selected="True">Don't set</option>
4427 <option value="set">Set value(s)</option>
4428 </param>
4429 <when value="no_set">
4430 </when>
4431 <when value="set">
4432
4433 <param name="oxford_single_chr_MOD_0_0" type="text" label="chr name" value="" optional="True" argument="chr name" help=""/>
4434 </when>
4435 </conditional>
4436 <conditional name="CONDITIONAL_missing_code">
4437 <param name="CONDITIONAL_SELECT_missing_code" type="select" label="Set Missing code" help="Comma-delimited list of missing phenotype (alias: --missing_code) values for Oxford-format import (default 'NA')." argument="--missing-code">
4438 <option value="no_set" selected="True">Don't set</option>
4439 <option value="set">Set value(s)</option>
4440 </param>
4441 <when value="no_set">
4442 </when>
4443 <when value="set">
4444
4445 <param name="missing_code_MOD_0_0" type="text" label="string list" value="" optional="False" argument="string list" help=""/>
4446 </when>
4447 </conditional>
4448 <conditional name="CONDITIONAL_hard_call_threshold">
4449 <param name="CONDITIONAL_SELECT_hard_call_threshold" type="select" label="Set Hard call threshold" help="When importing dosage data, a hardcall is normally saved when the distance from the nearest hardcall, defined as 0.5 * sum_i |x_i - round(x_i)| (where the x_i's are 0..2 allele dosages), is not greater than 0.1. You can adjust this threshold by providing a numeric parameter to --hard-call-threshold. You can also use this with --make-[b]pgen to alter the saved hardcalls while leaving the dosages untouched, or --make-bed to tweak hardcall export. " argument="--hard-call-threshold">
4450 <option value="no_set" selected="True">Don't set</option>
4451 <option value="set">Set value(s)</option>
4452 </param>
4453 <when value="no_set">
4454 </when>
4455 <when value="set">
4456
4457 <param name="hard_call_threshold_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4458 </when>
4459 </conditional>
4460 <conditional name="CONDITIONAL_dosage_erase_threshold">
4461 <param name="CONDITIONAL_SELECT_dosage_erase_threshold" type="select" label="Set Dosage erase threshold" help="--hard-call-threshold normally preserves the original dosages, and several PLINK 2 commands use them when they're available. Use --dosage-erase-threshold to make PLINK 2 erase dosages and keep only hardcalls when distance-from-hardcall &lt;= the given level. " argument="--dosage-erase-threshold">
4462 <option value="no_set" selected="True">Don't set</option>
4463 <option value="set">Set value(s)</option>
4464 </param>
4465 <when value="no_set">
4466 </when>
4467 <when value="set">
4468
4469 <param name="dosage_erase_threshold_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4470 </when>
4471 </conditional>
4472 <conditional name="CONDITIONAL_import_dosage_certainty">
4473 <param name="CONDITIONAL_SELECT_import_dosage_certainty" type="select" label="Set Import dosage certainty" help="The PLINK 2 file format currently supports a single dosage for each allele. Some other dosage file formats include a separate probability for every possible genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52, P(1/1)=0.28}, a highly uncertain call that is nevertheless treated as a hardcall under '--hard-call-threshold 0.1'. To make PLINK 2 treat a dosage as missing whenever the largest probability is less than a threshold, use --import-dosage-certainty. " argument="--import-dosage-certainty">
4474 <option value="no_set" selected="True">Don't set</option>
4475 <option value="set">Set value(s)</option>
4476 </param>
4477 <when value="no_set">
4478 </when>
4479 <when value="set">
4480
4481 <param name="import_dosage_certainty_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4482 </when>
4483 </conditional>
4484 <conditional name="CONDITIONAL_input_missing_genotype">
4485 <param name="CONDITIONAL_SELECT_input_missing_genotype" type="select" label="Set Input missing genotype" help="'.' is always interpreted as a missing genotype code in input files. By default, '0' also is; you can change this second missing code with --input-missing-genotype. " argument="--input-missing-genotype">
4486 <option value="no_set" selected="True">Don't set</option>
4487 <option value="set">Set value(s)</option>
4488 </param>
4489 <when value="no_set">
4490 </when>
4491 <when value="set">
4492
4493 <param name="input_missing_genotype_MOD_0_0" type="text" label="c" value="" optional="True" argument="c" help=""/>
4494 </when>
4495 </conditional>
4496 <conditional name="CONDITIONAL_allow_extra_chr">
4497 <param name="CONDITIONAL_SELECT_allow_extra_chr" type="select" label="Set Allow extra chr" help="Permit unrecognized chromosome codes (alias --aec). " argument="--allow-extra-chr">
4498 <option value="no_set" selected="True">Don't set</option>
4499 <option value="set">Set value(s)</option>
4500 </param>
4501 <when value="no_set">
4502 </when>
4503 <when value="set">
4504
4505 </when>
4506 </conditional>
4507 <conditional name="CONDITIONAL_chr_set">
4508 <param name="CONDITIONAL_SELECT_chr_set" type="select" label="Set Chr set" help="Specify a nonhuman chromosome set. The first parameter sets the number of diploid autosome pairs if positive, or haploid chromosomes if negative. Given diploid autosomes, the remaining modifiers indicate the absence of the named non-autosomal chromosomes." argument="--chr-set">
4509 <option value="no_set" selected="True">Don't set</option>
4510 <option value="set">Set value(s)</option>
4511 </param>
4512 <when value="no_set">
4513 </when>
4514 <when value="set">
4515
4516 <param name="chr_set_MOD_0_0" type="text" label="autosome ct" value="" optional="True" argument="autosome ct" help=""/>
4517 <param name="chr_set_MOD_1_0" type="text" label="'no-x'" value="" optional="False" argument="'no-x'" help=""/>
4518 <param name="chr_set_MOD_2_0" type="text" label="'no-y'" value="" optional="False" argument="'no-y'" help=""/>
4519 <param name="chr_set_MOD_3_0" type="text" label="'no-xy'" value="" optional="False" argument="'no-xy'" help=""/>
4520 <param name="chr_set_MOD_4_0" type="text" label="'no-mt'" value="" optional="False" argument="'no-mt'" help=""/>
4521 </when>
4522 </conditional>
4523 <conditional name="CONDITIONAL_cow">
4524 <param name="CONDITIONAL_SELECT_cow" type="select" label="Set Cow" help="Shortcuts for those species. " argument="--cow">
4525 <option value="no_set" selected="True">Don't set</option>
4526 <option value="set">Set value(s)</option>
4527 </param>
4528 <when value="no_set">
4529 </when>
4530 <when value="set">
4531
4532 </when>
4533 </conditional>
4534 <conditional name="CONDITIONAL_dog">
4535 <param name="CONDITIONAL_SELECT_dog" type="select" label="Set Dog" help="Shortcuts for those species. " argument="--dog">
4536 <option value="no_set" selected="True">Don't set</option>
4537 <option value="set">Set value(s)</option>
4538 </param>
4539 <when value="no_set">
4540 </when>
4541 <when value="set">
4542
4543 </when>
4544 </conditional>
4545 <conditional name="CONDITIONAL_horse">
4546 <param name="CONDITIONAL_SELECT_horse" type="select" label="Set Horse" help="Shortcuts for those species. " argument="--horse">
4547 <option value="no_set" selected="True">Don't set</option>
4548 <option value="set">Set value(s)</option>
4549 </param>
4550 <when value="no_set">
4551 </when>
4552 <when value="set">
4553
4554 </when>
4555 </conditional>
4556 <conditional name="CONDITIONAL_mouse">
4557 <param name="CONDITIONAL_SELECT_mouse" type="select" label="Set Mouse" help="Shortcuts for those species. " argument="--mouse">
4558 <option value="no_set" selected="True">Don't set</option>
4559 <option value="set">Set value(s)</option>
4560 </param>
4561 <when value="no_set">
4562 </when>
4563 <when value="set">
4564
4565 </when>
4566 </conditional>
4567 <conditional name="CONDITIONAL_rice">
4568 <param name="CONDITIONAL_SELECT_rice" type="select" label="Set Rice" help="Shortcuts for those species. " argument="--rice">
4569 <option value="no_set" selected="True">Don't set</option>
4570 <option value="set">Set value(s)</option>
4571 </param>
4572 <when value="no_set">
4573 </when>
4574 <when value="set">
4575
4576 </when>
4577 </conditional>
4578 <conditional name="CONDITIONAL_sheep">
4579 <param name="CONDITIONAL_SELECT_sheep" type="select" label="Set Sheep" help="Shortcuts for those species. " argument="--sheep">
4580 <option value="no_set" selected="True">Don't set</option>
4581 <option value="set">Set value(s)</option>
4582 </param>
4583 <when value="no_set">
4584 </when>
4585 <when value="set">
4586
4587 </when>
4588 </conditional>
4589 <conditional name="CONDITIONAL_autosome_num">
4590 <param name="CONDITIONAL_SELECT_autosome_num" type="select" label="Set Autosome num" help="Alias for '--chr-set &lt;value&gt; no-y no-xy no-mt'. " argument="--autosome-num">
4591 <option value="no_set" selected="True">Don't set</option>
4592 <option value="set">Set value(s)</option>
4593 </param>
4594 <when value="no_set">
4595 </when>
4596 <when value="set">
4597
4598 <param name="autosome_num_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4599 </when>
4600 </conditional>
4601 <conditional name="CONDITIONAL_human">
4602 <param name="CONDITIONAL_SELECT_human" type="select" label="Set Human" help="Explicitly specify human chromosome set, and make output .pvar/VCF files include a ##chrSet header line. (.pvar/VCF output files automatically include ##chrSet when a nonhuman set is specified.) " argument="--human">
4603 <option value="no_set" selected="True">Don't set</option>
4604 <option value="set">Set value(s)</option>
4605 </param>
4606 <when value="no_set">
4607 </when>
4608 <when value="set">
4609
4610 </when>
4611 </conditional>
4612 <conditional name="CONDITIONAL_chr_override">
4613 <param name="CONDITIONAL_SELECT_chr_override" type="select" label="Set Chr override" help="By default, if --chr-set/--autosome-num/--cow/etc. conflicts with an input file ##chrSet header line, PLINK 2 will error out. --chr-override with no parameter causes the command line to take precedence; '--chr-override file' defers to the file. " argument="--chr-override">
4614 <option value="no_set" selected="True">Don't set</option>
4615 <option value="set">Set value(s)</option>
4616 </param>
4617 <when value="no_set">
4618 </when>
4619 <when value="set">
4620
4621 <param name="chr_override_MOD_0_0" type="text" label="'file'" value="" optional="False" argument="'file'" help=""/>
4622 </when>
4623 </conditional>
4624 <conditional name="CONDITIONAL_var_min_qual">
4625 <param name="CONDITIONAL_SELECT_var_min_qual" type="select" label="Set Var min qual" help="Skip variants with low/missing QUAL. " argument="--var-min-qual">
4626 <option value="no_set" selected="True">Don't set</option>
4627 <option value="set">Set value(s)</option>
4628 </param>
4629 <when value="no_set">
4630 </when>
4631 <when value="set">
4632
4633 <param name="var_min_qual_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4634 </when>
4635 </conditional>
4636 <conditional name="CONDITIONAL_var_filter">
4637 <param name="CONDITIONAL_SELECT_var_filter" type="select" label="Set Var filter" help="Skip variants which have FILTER failures. " argument="--var-filter">
4638 <option value="no_set" selected="True">Don't set</option>
4639 <option value="set">Set value(s)</option>
4640 </param>
4641 <when value="no_set">
4642 </when>
4643 <when value="set">
4644
4645 <param name="var_filter_MOD_0_0" type="text" label="exception(s)..." value="" optional="False" argument="exception(s)..." help="Multiple values are allowed"/>
4646 </when>
4647 </conditional>
4648 <conditional name="CONDITIONAL_extract_if_info">
4649 <param name="CONDITIONAL_SELECT_extract_if_info" type="select" label="Set Extract if info" help="Exclude variants which don't/do satisfy " argument="--extract-if-info">
4650 <option value="no_set" selected="True">Don't set</option>
4651 <option value="set">Set value(s)</option>
4652 </param>
4653 <when value="no_set">
4654 </when>
4655 <when value="set">
4656
4657 <param name="extract_if_info_MOD_0_0" type="text" label="key" value="" optional="True" argument="key" help=""/>
4658 <param name="extract_if_info_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/>
4659 <param name="extract_if_info_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4660 </when>
4661 </conditional>
4662 <conditional name="CONDITIONAL_exclude_if_info">
4663 <param name="CONDITIONAL_SELECT_exclude_if_info" type="select" label="Set Exclude if info" help='(aliases: --extract-if, e.g. --exclude-if) --extract-if-info "VT == SNP" Unless the operator is !=, the predicate always evaluates to false when the key is missing.' argument="--exclude-if-info">
4664 <option value="no_set" selected="True">Don't set</option>
4665 <option value="set">Set value(s)</option>
4666 </param>
4667 <when value="no_set">
4668 </when>
4669 <when value="set">
4670
4671 <param name="exclude_if_info_MOD_0_0" type="text" label="key" value="" optional="True" argument="key" help=""/>
4672 <param name="exclude_if_info_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/>
4673 <param name="exclude_if_info_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
4674 </when>
4675 </conditional>
4676 <conditional name="CONDITIONAL_require_info">
4677 <param name="CONDITIONAL_SELECT_require_info" type="select" label="Set Require info" help="Exclude variants based on nonexistence " argument="--require-info">
4678 <option value="no_set" selected="True">Don't set</option>
4679 <option value="set">Set value(s)</option>
4680 </param>
4681 <when value="no_set">
4682 </when>
4683 <when value="set">
4684
4685 <param name="require_info_MOD_0_0" type="text" label="key(s)..." value="" optional="True" argument="key(s)..." help="Multiple values are allowed"/>
4686 </when>
4687 </conditional>
4688 <conditional name="CONDITIONAL_require_no_info">
4689 <param name="CONDITIONAL_SELECT_require_no_info" type="select" label="Set Require no info" help="" argument="--require-no-info">
4690 <option value="no_set" selected="True">Don't set</option>
4691 <option value="set">Set value(s)</option>
4692 </param>
4693 <when value="no_set">
4694 </when>
4695 <when value="set">
4696
4697 <param name="require_no_info_MOD_0_0" type="text" label="key(s)..." value="" optional="True" argument="key(s)..." help="Multiple values are allowed"/>
4698 <param name="require_no_info_MOD_1_0" type="text" label="key" value="" optional="True" argument="key" help=""/>
4699 </when>
4700 </conditional>
4701 <conditional name="CONDITIONAL_extract_col_cond">
4702 <param name="CONDITIONAL_SELECT_extract_col_cond" type="select" label="Set Extract col cond" help="" argument="--extract-col-cond">
4703 <option value="no_set" selected="True">Don't set</option>
4704 <option value="set">Set value(s)</option>
4705 </param>
4706 <when value="no_set">
4707 </when>
4708 <when value="set">
4709
4710 <param name="extract_col_cond_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
4711 <param name="extract_col_cond_MOD_1_0" type="text" label="valcol" value="" optional="False" argument="valcol" help=""/>
4712 <param name="extract_col_cond_MOD_2_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/>
4713 <param name="extract_col_cond_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
4714 </when>
4715 </conditional>
4716 <conditional name="CONDITIONAL_extract_col_cond_match">
4717 <param name="CONDITIONAL_SELECT_extract_col_cond_match" type="select" label="Set Extract col cond match" help="" argument="--extract-col-cond-match">
4718 <option value="no_set" selected="True">Don't set</option>
4719 <option value="set">Set value(s)</option>
4720 </param>
4721 <when value="no_set">
4722 </when>
4723 <when value="set">
4724
4725 <param name="extract_col_cond_match_MOD_0_0" type="text" label="(sub)string(s)..." value="" optional="True" argument="(sub)string(s)..." help="Multiple values are allowed"/>
4726 </when>
4727 </conditional>
4728 <conditional name="CONDITIONAL_extract_col_cond_mismatch">
4729 <param name="CONDITIONAL_SELECT_extract_col_cond_mismatch" type="select" label="Set Extract col cond mismatch" help="" argument="--extract-col-cond-mismatch">
4730 <option value="no_set" selected="True">Don't set</option>
4731 <option value="set">Set value(s)</option>
4732 </param>
4733 <when value="no_set">
4734 </when>
4735 <when value="set">
4736
4737 <param name="extract_col_cond_mismatch_MOD_0_0" type="text" label="(sub)string(s)..." value="" optional="True" argument="(sub)string(s)..." help="Multiple values are allowed"/>
4738 </when>
4739 </conditional>
4740 <param name="extract_col_cond_substr" type="boolean" label="Extract col cond substr" truevalue="--extract-col-cond-substr" falsevalue="" optional="true" argument="--extract-col-cond-substr" help="" checked="False"/>
4741 <conditional name="CONDITIONAL_extract_col_cond_min">
4742 <param name="CONDITIONAL_SELECT_extract_col_cond_min" type="select" label="Set Extract col cond min" help="" argument="--extract-col-cond-min">
4743 <option value="no_set" selected="True">Don't set</option>
4744 <option value="set">Set value(s)</option>
4745 </param>
4746 <when value="no_set">
4747 </when>
4748 <when value="set">
4749
4750 <param name="extract_col_cond_min_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/>
4751 </when>
4752 </conditional>
4753 <conditional name="CONDITIONAL_extract_col_cond_max">
4754 <param name="CONDITIONAL_SELECT_extract_col_cond_max" type="select" label="Set Extract col cond max" help="Exclude all variants without a value-column entry satisfying a condition. * By default, values are read from column 2 of the file, and variant IDs are read from column 1. * Three types of conditions are supported: * When --extract-col-cond-match is specified without --extract-col-cond-substr, the value is checked for equality with the given strings, and kept iff one of them matches. Similarly, --extract-col-cond-mismatch without --extract-col-cond-substr causes the variant to be kept iff the value matches none of the given strings. * When --extract-col-cond-match and/or -mismatch are specified with --extract-col-cond-substr, the variant is kept iff none of the --extract-col-cond-mismatch substrings are contained in the value, and either --extract-col-cond-match was unspecified or at least one of its substrings is contained. * Otherwise, the value is interpreted as a number, and the variant is kept if the number is in [&lt;min&gt;, &lt;max&gt;] (default min=0, max=DBL_MAX)." argument="--extract-col-cond-max">
4755 <option value="no_set" selected="True">Don't set</option>
4756 <option value="set">Set value(s)</option>
4757 </param>
4758 <when value="no_set">
4759 </when>
4760 <when value="set">
4761
4762 <param name="extract_col_cond_max_MOD_0_0" type="text" label="max" value="" optional="True" argument="max" help=""/>
4763 </when>
4764 </conditional>
4765 <conditional name="CONDITIONAL_pheno">
4766 <param name="CONDITIONAL_SELECT_pheno" type="select" label="Set Pheno" help="Specify additional phenotype/covariate file. Comma-delimited files with a header line are now permitted. " argument="--pheno">
4767 <option value="no_set" selected="True">Don't set</option>
4768 <option value="set">Set value(s)</option>
4769 </param>
4770 <when value="no_set">
4771 </when>
4772 <when value="set">
4773
4774 <param name="pheno_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/>
4775 <param name="pheno_MOD_1_0" type="data" format="plink.pheno" label="f" multiple="False" optional="True" argument="f"/>
4776 </when>
4777 </conditional>
4778 <conditional name="CONDITIONAL_pheno_name">
4779 <param name="CONDITIONAL_SELECT_pheno_name" type="select" label="Set Pheno name" help="Only load the designated phenotype(s) from the --pheno (if one was specified) or .psam (if no --pheno) file. Separate multiple names with spaces or commas, and use dashes to designate ranges. " argument="--pheno-name">
4780 <option value="no_set" selected="True">Don't set</option>
4781 <option value="set">Set value(s)</option>
4782 </param>
4783 <when value="no_set">
4784 </when>
4785 <when value="set">
4786
4787 <param name="pheno_name_MOD_0_0" type="text" label="name..." value="" optional="True" argument="name..." help="Multiple values are allowed"/>
4788 </when>
4789 </conditional>
4790 <conditional name="CONDITIONAL_pheno_col_nums">
4791 <param name="CONDITIONAL_SELECT_pheno_col_nums" type="select" label="Set Pheno col nums" help="Only load the phenotype(s) in the designated column number(s) from the --pheno file. " argument="--pheno-col-nums">
4792 <option value="no_set" selected="True">Don't set</option>
4793 <option value="set">Set value(s)</option>
4794 </param>
4795 <when value="no_set">
4796 </when>
4797 <when value="set">
4798
4799 <param name="pheno_col_nums_MOD_0_0" type="text" label="#..." value="" optional="True" argument="#..." help="Multiple values are allowed"/>
4800 </when>
4801 </conditional>
4802 <conditional name="CONDITIONAL_no_psam_pheno">
4803 <param name="CONDITIONAL_SELECT_no_psam_pheno" type="select" label="Set No psam pheno" help="Ignore phenotype(s) in .psam/.fam file. " argument="--no-psam-pheno">
4804 <option value="no_set" selected="True">Don't set</option>
4805 <option value="set">Set value(s)</option>
4806 </param>
4807 <when value="no_set">
4808 </when>
4809 <when value="set">
4810
4811 </when>
4812 </conditional>
4813 <conditional name="CONDITIONAL_strict_sid0">
4814 <param name="CONDITIONAL_SELECT_strict_sid0" type="select" label="Set Strict sid0" help="By default, if there is no SID column in the .psam/.fam (or --update-ids) file, but there is one in another input file (for e.g. --keep/--remove), the latter SID column is ignored; sample IDs are considered matching as long as FID and IID are equal (with missing FID treated as '0'). If you also want to require SID = '0' for a sample ID match in this situation, add --strict-sid0. " argument="--strict-sid0">
4815 <option value="no_set" selected="True">Don't set</option>
4816 <option value="set">Set value(s)</option>
4817 </param>
4818 <when value="no_set">
4819 </when>
4820 <when value="set">
4821
4822 </when>
4823 </conditional>
4824 <conditional name="CONDITIONAL_input_missing_phenotype">
4825 <param name="CONDITIONAL_SELECT_input_missing_phenotype" type="select" label="Set Input missing phenotype" help="Set nonzero number to treat as a missing pheno/covar in input files (default -9). " argument="--input-missing-phenotype">
4826 <option value="no_set" selected="True">Don't set</option>
4827 <option value="set">Set value(s)</option>
4828 </param>
4829 <when value="no_set">
4830 </when>
4831 <when value="set">
4832
4833 <param name="input_missing_phenotype_MOD_0_0" type="text" label="v" value="" optional="True" argument="v" help=""/>
4834 </when>
4835 </conditional>
4836 <conditional name="CONDITIONAL_no_input_missing_phenotype">
4837 <param name="CONDITIONAL_SELECT_no_input_missing_phenotype" type="select" label="Set No input missing phenotype" help="Don't treat any nonzero number as a missing pheno/covar. ('NA'/'nan' are still treated as missing.) " argument="--no-input-missing-phenotype">
4838 <option value="no_set" selected="True">Don't set</option>
4839 <option value="set">Set value(s)</option>
4840 </param>
4841 <when value="no_set">
4842 </when>
4843 <when value="set">
4844
4845 </when>
4846 </conditional>
4847 <conditional name="CONDITIONAL_GALAXY_1">
4848 <param name="CONDITIONAL_SELECT_GALAXY_1" type="select" label="Set 1" help="Expect case/control phenotypes in input files to be coded as 0 = control, 1 = case, instead of the usual 0 = missing, 1 = ctrl, 2 = case. (Unlike PLINK 1.x, this does not force all phenotypes to be interpreted as case/ctrl.) " argument="--1">
4849 <option value="no_set" selected="True">Don't set</option>
4850 <option value="set">Set value(s)</option>
4851 </param>
4852 <when value="no_set">
4853 </when>
4854 <when value="set">
4855
4856 </when>
4857 </conditional>
4858 <conditional name="CONDITIONAL_missing_catname">
4859 <param name="CONDITIONAL_SELECT_missing_catname" type="select" label="Set Missing catname" help="Set missing-categorical-phenotype string (case-sensitive, default 'NONE'). " argument="--missing-catname">
4860 <option value="no_set" selected="True">Don't set</option>
4861 <option value="set">Set value(s)</option>
4862 </param>
4863 <when value="no_set">
4864 </when>
4865 <when value="set">
4866
4867 <param name="missing_catname_MOD_0_0" type="text" label="str" value="" optional="True" argument="str" help=""/>
4868 </when>
4869 </conditional>
4870 <conditional name="CONDITIONAL_covar">
4871 <param name="CONDITIONAL_SELECT_covar" type="select" label="Set Covar" help="Specify additional covariate file. Comma-delimited files with a header line are now permitted. " argument="--covar">
4872 <option value="no_set" selected="True">Don't set</option>
4873 <option value="set">Set value(s)</option>
4874 </param>
4875 <when value="no_set">
4876 </when>
4877 <when value="set">
4878
4879 <param name="covar_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/>
4880 <param name="covar_MOD_1_0" type="data" format="plink.covar" label="f" multiple="False" optional="True" argument="f"/>
4881 </when>
4882 </conditional>
4883 <conditional name="CONDITIONAL_covar_name">
4884 <param name="CONDITIONAL_SELECT_covar_name" type="select" label="Set Covar name" help="Only load the designated covariate(s) from the --covar (if one was specified), --pheno (if no --covar), or .psam (if no --covar or --pheno) file. " argument="--covar-name">
4885 <option value="no_set" selected="True">Don't set</option>
4886 <option value="set">Set value(s)</option>
4887 </param>
4888 <when value="no_set">
4889 </when>
4890 <when value="set">
4891
4892 <param name="covar_name_MOD_0_0" type="text" label="name..." value="" optional="True" argument="name..." help="Multiple values are allowed"/>
4893 </when>
4894 </conditional>
4895 <conditional name="CONDITIONAL_covar_col_nums">
4896 <param name="CONDITIONAL_SELECT_covar_col_nums" type="select" label="Set Covar col nums" help="Only load the covariate(s) in the designated column number(s) from the --covar (if one was specified) or --pheno (if no --covar) file. " argument="--covar-col-nums">
4897 <option value="no_set" selected="True">Don't set</option>
4898 <option value="set">Set value(s)</option>
4899 </param>
4900 <when value="no_set">
4901 </when>
4902 <when value="set">
4903
4904 <param name="covar_col_nums_MOD_0_0" type="text" label="#..." value="" optional="True" argument="#..." help="Multiple values are allowed"/>
4905 </when>
4906 </conditional>
4907 <conditional name="CONDITIONAL_within">
4908 <param name="CONDITIONAL_SELECT_within" type="select" label="Set Within" help="Import a PLINK 1.x categorical phenotype. (Phenotype name defaults to 'CATPHENO'.) * If any numeric values are present, ALL values must be numeric. In that case, 'C' is added in front of all category names. * 'NA' is treated as a missing value. " argument="--within">
4909 <option value="no_set" selected="True">Don't set</option>
4910 <option value="set">Set value(s)</option>
4911 </param>
4912 <when value="no_set">
4913 </when>
4914 <when value="set">
4915
4916 <param name="within_MOD_0_0" type="data" format="tabular" label="f" multiple="False" optional="True" argument="f"/>
4917 <param name="within_MOD_1_0" type="text" label="new pheno name" value="" optional="False" argument="new pheno name" help=""/>
4918 </when>
4919 </conditional>
4920 <conditional name="CONDITIONAL_mwithin">
4921 <param name="CONDITIONAL_SELECT_mwithin" type="select" label="Set Mwithin" help="Load --within categories from column n+2. " argument="--mwithin">
4922 <option value="no_set" selected="True">Don't set</option>
4923 <option value="set">Set value(s)</option>
4924 </param>
4925 <when value="no_set">
4926 </when>
4927 <when value="set">
4928
4929 <param name="mwithin_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/>
4930 </when>
4931 </conditional>
4932 <conditional name="CONDITIONAL_family">
4933 <param name="CONDITIONAL_SELECT_family" type="select" label="Set Family" help="Create a categorical phenotype from FID. Restrictions on and handling of numeric values are the same as for --within. " argument="--family">
4934 <option value="no_set" selected="True">Don't set</option>
4935 <option value="set">Set value(s)</option>
4936 </param>
4937 <when value="no_set">
4938 </when>
4939 <when value="set">
4940
4941 <param name="family_MOD_0_0" type="text" label="new pheno name" value="" optional="False" argument="new pheno name" help=""/>
4942 </when>
4943 </conditional>
4944 <conditional name="CONDITIONAL_family_missing_catname">
4945 <param name="CONDITIONAL_SELECT_family_missing_catname" type="select" label="Set Family missing catname" help="Make --family treat the specified FID as missing. " argument="--family-missing-catname">
4946 <option value="no_set" selected="True">Don't set</option>
4947 <option value="set">Set value(s)</option>
4948 </param>
4949 <when value="no_set">
4950 </when>
4951 <when value="set">
4952
4953 <param name="family_missing_catname_MOD_0_0" type="text" label="nm" value="" optional="True" argument="nm" help=""/>
4954 </when>
4955 </conditional>
4956 <conditional name="CONDITIONAL_keep">
4957 <param name="CONDITIONAL_SELECT_keep" type="select" label="Set Keep" help="Exclude all samples not named in a file. " argument="--keep">
4958 <option value="no_set" selected="True">Don't set</option>
4959 <option value="set">Set value(s)</option>
4960 </param>
4961 <when value="no_set">
4962 </when>
4963 <when value="set">
4964
4965 <param name="keep_MOD_0_0" type="text" label="fname..." value="" optional="True" argument="fname..." help="Multiple values are allowed"/>
4966 </when>
4967 </conditional>
4968 <conditional name="CONDITIONAL_remove">
4969 <param name="CONDITIONAL_SELECT_remove" type="select" label="Set Remove" help="Exclude all samples named in a file. " argument="--remove">
4970 <option value="no_set" selected="True">Don't set</option>
4971 <option value="set">Set value(s)</option>
4972 </param>
4973 <when value="no_set">
4974 </when>
4975 <when value="set">
4976
4977 <param name="remove_MOD_0_0" type="text" label="fname..." value="" optional="True" argument="fname..." help="Multiple values are allowed"/>
4978 </when>
4979 </conditional>
4980 <conditional name="CONDITIONAL_keep_fam">
4981 <param name="CONDITIONAL_SELECT_keep_fam" type="select" label="Set Keep fam" help="Exclude all families not named in a file. " argument="--keep-fam">
4982 <option value="no_set" selected="True">Don't set</option>
4983 <option value="set">Set value(s)</option>
4984 </param>
4985 <when value="no_set">
4986 </when>
4987 <when value="set">
4988
4989 <param name="keep_fam_MOD_0_0" type="text" label="fn..." value="" optional="True" argument="fn..." help="Multiple values are allowed"/>
4990 </when>
4991 </conditional>
4992 <conditional name="CONDITIONAL_remove_fam">
4993 <param name="CONDITIONAL_SELECT_remove_fam" type="select" label="Set Remove fam" help="Exclude all families named in a file. " argument="--remove-fam">
4994 <option value="no_set" selected="True">Don't set</option>
4995 <option value="set">Set value(s)</option>
4996 </param>
4997 <when value="no_set">
4998 </when>
4999 <when value="set">
5000
5001 <param name="remove_fam_MOD_0_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/>
5002 </when>
5003 </conditional>
5004 <conditional name="CONDITIONAL_extract">
5005 <param name="CONDITIONAL_SELECT_extract" type="select" label="Set Extract" help="Usually excludes all variants (not) named " argument="--extract">
5006 <option value="no_set" selected="True">Don't set</option>
5007 <option value="set">Set value(s)</option>
5008 </param>
5009 <when value="no_set">
5010 </when>
5011 <when value="set">
5012
5013 <conditional name="CONDITIONAL_extract_MOD_0">
5014 <param name="CONDITIONAL_SELECT_extract_MOD_0" type="select" label="How to set Extract">
5015 <option value="no_set" selected="True">Don't set</option>
5016 <option value="from_list">Select from list</option>
5017
5018 </param>
5019 <when value="no_set">
5020 </when>
5021
5022 <when value="from_list">
5023 <param name="extract_MOD_0" type="select" label="Select value">
5024 <option value="{bed0">{bed0</option>
5025 <option value="bed1}">bed1}</option>
5026 </param>
5027 </when>
5028 </conditional>
5029 <param name="extract_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/>
5030 </when>
5031 </conditional>
5032 <conditional name="CONDITIONAL_exclude">
5033 <param name="CONDITIONAL_SELECT_exclude" type="select" label="Set Exclude" help="" argument="--exclude">
5034 <option value="no_set" selected="True">Don't set</option>
5035 <option value="set">Set value(s)</option>
5036 </param>
5037 <when value="no_set">
5038 </when>
5039 <when value="set">
5040
5041 <conditional name="CONDITIONAL_exclude_MOD_0">
5042 <param name="CONDITIONAL_SELECT_exclude_MOD_0" type="select" label="How to set Exclude">
5043 <option value="no_set" selected="True">Don't set</option>
5044 <option value="from_list">Select from list</option>
5045
5046 </param>
5047 <when value="no_set">
5048 </when>
5049
5050 <when value="from_list">
5051 <param name="exclude_MOD_0" type="select" label="Select value">
5052 <option value="{bed0">{bed0</option>
5053 <option value="bed1}">bed1}</option>
5054 </param>
5055 </when>
5056 </conditional>
5057 <param name="exclude_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/>
5058 </when>
5059 </conditional>
5060 <conditional name="CONDITIONAL_extract_intersect">
5061 <param name="CONDITIONAL_SELECT_extract_intersect" type="select" label="Set Extract intersect" help="Just like --extract, except that a variant must be in the intersection, rather than just the union, of the files to remain. " argument="--extract-intersect">
5062 <option value="no_set" selected="True">Don't set</option>
5063 <option value="set">Set value(s)</option>
5064 </param>
5065 <when value="no_set">
5066 </when>
5067 <when value="set">
5068
5069 <conditional name="CONDITIONAL_extract_intersect_MOD_0">
5070 <param name="CONDITIONAL_SELECT_extract_intersect_MOD_0" type="select" label="How to set Extract intersect">
5071 <option value="no_set" selected="True">Don't set</option>
5072 <option value="from_list">Select from list</option>
5073
5074 </param>
5075 <when value="no_set">
5076 </when>
5077
5078 <when value="from_list">
5079 <param name="extract_intersect_MOD_0" type="select" label="Select value">
5080 <option value="{bed0">{bed0</option>
5081 <option value="bed1}">bed1}</option>
5082 </param>
5083 </when>
5084 </conditional>
5085 <param name="extract_intersect_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/>
5086 </when>
5087 </conditional>
5088 <conditional name="CONDITIONAL_keep_cats">
5089 <param name="CONDITIONAL_SELECT_keep_cats" type="select" label="Set Keep cats" help="These can be used individually or in combination " argument="--keep-cats">
5090 <option value="no_set" selected="True">Don't set</option>
5091 <option value="set">Set value(s)</option>
5092 </param>
5093 <when value="no_set">
5094 </when>
5095 <when value="set">
5096
5097 <param name="keep_cats_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
5098 </when>
5099 </conditional>
5100 <conditional name="CONDITIONAL_keep_cat_names">
5101 <param name="CONDITIONAL_SELECT_keep_cat_names" type="select" label="Set Keep cat names" help="" argument="--keep-cat-names">
5102 <option value="no_set" selected="True">Don't set</option>
5103 <option value="set">Set value(s)</option>
5104 </param>
5105 <when value="no_set">
5106 </when>
5107 <when value="set">
5108
5109 <param name="keep_cat_names_MOD_0_0" type="text" label="nm..." value="" optional="True" argument="nm..." help="Multiple values are allowed"/>
5110 </when>
5111 </conditional>
5112 <conditional name="CONDITIONAL_keep_cat_pheno">
5113 <param name="CONDITIONAL_SELECT_keep_cat_pheno" type="select" label="Set Keep cat pheno" help="If more than one categorical phenotype is loaded, or you wish to filter on a categorical covariate, --keep-cat-pheno must be used to specify which phenotype/covariate --keep-cats and --keep-cat-names apply to. " argument="--keep-cat-pheno">
5114 <option value="no_set" selected="True">Don't set</option>
5115 <option value="set">Set value(s)</option>
5116 </param>
5117 <when value="no_set">
5118 </when>
5119 <when value="set">
5120
5121 <param name="keep_cat_pheno_MOD_0_0" type="text" label="pheno" value="" optional="True" argument="pheno" help=""/>
5122 </when>
5123 </conditional>
5124 <conditional name="CONDITIONAL_remove_cats">
5125 <param name="CONDITIONAL_SELECT_remove_cats" type="select" label="Set Remove cats" help="Exclude all categories named in the file. " argument="--remove-cats">
5126 <option value="no_set" selected="True">Don't set</option>
5127 <option value="set">Set value(s)</option>
5128 </param>
5129 <when value="no_set">
5130 </when>
5131 <when value="set">
5132
5133 <param name="remove_cats_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
5134 </when>
5135 </conditional>
5136 <conditional name="CONDITIONAL_remove_cat_names">
5137 <param name="CONDITIONAL_SELECT_remove_cat_names" type="select" label="Set Remove cat names" help="Exclude named categories. " argument="--remove-cat-names">
5138 <option value="no_set" selected="True">Don't set</option>
5139 <option value="set">Set value(s)</option>
5140 </param>
5141 <when value="no_set">
5142 </when>
5143 <when value="set">
5144
5145 <param name="remove_cat_names_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
5146 </when>
5147 </conditional>
5148 <conditional name="CONDITIONAL_remove_cat_pheno">
5149 <param name="CONDITIONAL_SELECT_remove_cat_pheno" type="select" label="Set Remove cat pheno" help="Specify pheno for --remove-cats/remove-cat-names. " argument="--remove-cat-pheno">
5150 <option value="no_set" selected="True">Don't set</option>
5151 <option value="set">Set value(s)</option>
5152 </param>
5153 <when value="no_set">
5154 </when>
5155 <when value="set">
5156
5157 <param name="remove_cat_pheno_MOD_0_0" type="text" label="phe" value="" optional="True" argument="phe" help=""/>
5158 </when>
5159 </conditional>
5160 <conditional name="CONDITIONAL_split_cat_pheno">
5161 <param name="CONDITIONAL_SELECT_split_cat_pheno" type="select" label="Set Split cat pheno" help="Split n-category phenotype(s) into n (or n-1, with 'omit-most'/'omit-last') binary phenotypes, with names of the form &lt;orig. pheno name&gt;=&lt;cat. name&gt;. (As a consequence, affected phenotypes and categories are not permitted to contain the '=' character.) * This happens after all sample filters. * If no phenotype or covariate names are provided, all categorical phenotypes (but not covariates) are processed. * By default, generated covariates are coded as 1=false, 2=true. To code them as 0=false, 1=true instead, add the 'covar-01' modifier." argument="--split-cat-pheno">
5162 <option value="no_set" selected="True">Don't set</option>
5163 <option value="set">Set value(s)</option>
5164 </param>
5165 <when value="no_set">
5166 </when>
5167 <when value="set">
5168
5169 <conditional name="CONDITIONAL_split_cat_pheno_MOD_0">
5170 <param name="CONDITIONAL_SELECT_split_cat_pheno_MOD_0" type="select" label="How to set Split cat pheno">
5171 <option value="no_set" selected="True">Don't set</option>
5172 <option value="from_list">Select from list</option>
5173
5174 </param>
5175 <when value="no_set">
5176 </when>
5177
5178 <when value="from_list">
5179 <param name="split_cat_pheno_MOD_0" type="select" label="Select value">
5180 <option value="{omit-most">{omit-most</option>
5181 <option value="omit-last}">omit-last}</option>
5182 </param>
5183 </when>
5184 </conditional>
5185 <param name="split_cat_pheno_MOD_1_0" type="text" label="'covar-01'" value="" optional="False" argument="'covar-01'" help=""/>
5186 <param name="split_cat_pheno_MOD_2_0" type="text" label="cat. pheno/covar name(s)..." value="" optional="False" argument="cat. pheno/covar name(s)..." help="Multiple values are allowed"/>
5187 </when>
5188 </conditional>
5189 <conditional name="CONDITIONAL_loop_cats">
5190 <param name="CONDITIONAL_SELECT_loop_cats" type="select" label="Set Loop cats" help="Run variant filters and subsequent operations on just the samples in the first category; then just the samples in the second category; and so on, for all categories in the named categorical phenotype. " argument="--loop-cats">
5191 <option value="no_set" selected="True">Don't set</option>
5192 <option value="set">Set value(s)</option>
5193 </param>
5194 <when value="no_set">
5195 </when>
5196 <when value="set">
5197
5198 <param name="loop_cats_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/>
5199 </when>
5200 </conditional>
5201 <conditional name="CONDITIONAL_no_id_header">
5202 <param name="CONDITIONAL_SELECT_no_id_header" type="select" label="Set No id header" help="Don't include a header line in .id output files. This normally forces two-column FID/IID output; add 'iid-only' to force just single-column IID. " argument="--no-id-header">
5203 <option value="no_set" selected="True">Don't set</option>
5204 <option value="set">Set value(s)</option>
5205 </param>
5206 <when value="no_set">
5207 </when>
5208 <when value="set">
5209
5210 <param name="no_id_header_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/>
5211 </when>
5212 </conditional>
5213 <conditional name="CONDITIONAL_variance_standardize">
5214 <param name="CONDITIONAL_SELECT_variance_standardize" type="select" label="Set Variance standardize" help="" argument="--variance-standardize">
5215 <option value="no_set" selected="True">Don't set</option>
5216 <option value="set">Set value(s)</option>
5217 </param>
5218 <when value="no_set">
5219 </when>
5220 <when value="set">
5221
5222 <param name="variance_standardize_MOD_0_0" type="text" label="pheno/covar name(s)..." value="" optional="False" argument="pheno/covar name(s)..." help="Multiple values are allowed"/>
5223 </when>
5224 </conditional>
5225 <conditional name="CONDITIONAL_covar_variance_standardize">
5226 <param name="CONDITIONAL_SELECT_covar_variance_standardize" type="select" label="Set Covar variance standardize" help="Linearly transform named covariates (and quantitative phenotypes, if --variance-standardize) to mean-zero, variance 1. If no parameters are provided, all possible phenotypes/covariates are affected. This is frequently necessary to prevent multicollinearity when dealing with covariates where abs(mean) is much larger than abs(standard deviation), such as year of birth." argument="--covar-variance-standardize">
5227 <option value="no_set" selected="True">Don't set</option>
5228 <option value="set">Set value(s)</option>
5229 </param>
5230 <when value="no_set">
5231 </when>
5232 <when value="set">
5233
5234 <param name="covar_variance_standardize_MOD_0_0" type="text" label="covar name(s)..." value="" optional="False" argument="covar name(s)..." help="Multiple values are allowed"/>
5235 </when>
5236 </conditional>
5237 <conditional name="CONDITIONAL_quantile_normalize">
5238 <param name="CONDITIONAL_SELECT_quantile_normalize" type="select" label="Set Quantile normalize" help="Force named covariates and quantitative " argument="--quantile-normalize">
5239 <option value="no_set" selected="True">Don't set</option>
5240 <option value="set">Set value(s)</option>
5241 </param>
5242 <when value="no_set">
5243 </when>
5244 <when value="set">
5245
5246 <param name="quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/>
5247 </when>
5248 </conditional>
5249 <conditional name="CONDITIONAL_pheno_quantile_normalize">
5250 <param name="CONDITIONAL_SELECT_pheno_quantile_normalize" type="select" label="Set Pheno quantile normalize" help="" argument="--pheno-quantile-normalize">
5251 <option value="no_set" selected="True">Don't set</option>
5252 <option value="set">Set value(s)</option>
5253 </param>
5254 <when value="no_set">
5255 </when>
5256 <when value="set">
5257
5258 <param name="pheno_quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/>
5259 </when>
5260 </conditional>
5261 <conditional name="CONDITIONAL_covar_quantile_normalize">
5262 <param name="CONDITIONAL_SELECT_covar_quantile_normalize" type="select" label="Set Covar quantile normalize" help="" argument="--covar-quantile-normalize">
5263 <option value="no_set" selected="True">Don't set</option>
5264 <option value="set">Set value(s)</option>
5265 </param>
5266 <when value="no_set">
5267 </when>
5268 <when value="set">
5269
5270 <param name="covar_quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/>
5271 </when>
5272 </conditional>
5273 <conditional name="CONDITIONAL_chr">
5274 <param name="CONDITIONAL_SELECT_chr" type="select" label="Set Chr" help="Exclude all variants not on the given chromosome(s). Valid choices for humans are 0 (unplaced), 1-22, X, Y, XY, MT, PAR1, and PAR2. Separate multiple chromosomes with spaces and/or commas, and use a dash (no adjacent spaces permitted) to denote a range, e.g. '--chr 1-4, 22, par1, x, par2'. " argument="--chr">
5275 <option value="no_set" selected="True">Don't set</option>
5276 <option value="set">Set value(s)</option>
5277 </param>
5278 <when value="no_set">
5279 </when>
5280 <when value="set">
5281
5282 <param name="chr_MOD_0_0" type="text" label="chr(s)..." value="" optional="True" argument="chr(s)..." help="Multiple values are allowed"/>
5283 </when>
5284 </conditional>
5285 <conditional name="CONDITIONAL_not_chr">
5286 <param name="CONDITIONAL_SELECT_not_chr" type="select" label="Set Not chr" help="Reverse of --chr (exclude variants on listed chromosomes). " argument="--not-chr">
5287 <option value="no_set" selected="True">Don't set</option>
5288 <option value="set">Set value(s)</option>
5289 </param>
5290 <when value="no_set">
5291 </when>
5292 <when value="set">
5293
5294 <param name="not_chr_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
5295 </when>
5296 </conditional>
5297 <conditional name="CONDITIONAL_autosome">
5298 <param name="CONDITIONAL_SELECT_autosome" type="select" label="Set Autosome" help="Exclude all non-autosomal variants. " argument="--autosome">
5299 <option value="no_set" selected="True">Don't set</option>
5300 <option value="set">Set value(s)</option>
5301 </param>
5302 <when value="no_set">
5303 </when>
5304 <when value="set">
5305
5306 </when>
5307 </conditional>
5308 <conditional name="CONDITIONAL_autosome_par">
5309 <param name="CONDITIONAL_SELECT_autosome_par" type="select" label="Set Autosome par" help="Exclude all non-autosomal variants, except those in a pseudo-autosomal region. " argument="--autosome-par">
5310 <option value="no_set" selected="True">Don't set</option>
5311 <option value="set">Set value(s)</option>
5312 </param>
5313 <when value="no_set">
5314 </when>
5315 <when value="set">
5316
5317 </when>
5318 </conditional>
5319 <conditional name="CONDITIONAL_snps_only">
5320 <param name="CONDITIONAL_SELECT_snps_only" type="select" label="Set Snps only" help="Exclude non-SNP variants. By default, SNP = all allele codes are single-character (so multiallelic variants with a mix of SNPs and non-SNPs are excluded; split your variants first if that's a problem). The 'just-acgt' modifier restricts SNP codes to {A,C,G,T,a,c,g,t,&lt;missing&gt;}. " argument="--snps-only">
5321 <option value="no_set" selected="True">Don't set</option>
5322 <option value="set">Set value(s)</option>
5323 </param>
5324 <when value="no_set">
5325 </when>
5326 <when value="set">
5327
5328 <param name="snps_only_MOD_0_0" type="text" label="'just-acgt'" value="" optional="False" argument="'just-acgt'" help=""/>
5329 </when>
5330 </conditional>
5331 <conditional name="CONDITIONAL_from">
5332 <param name="CONDITIONAL_SELECT_from" type="select" label="Set From" help="Use ID(s) to specify a variant range to load. When used " argument="--from">
5333 <option value="no_set" selected="True">Don't set</option>
5334 <option value="set">Set value(s)</option>
5335 </param>
5336 <when value="no_set">
5337 </when>
5338 <when value="set">
5339
5340 <param name="from_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/>
5341 </when>
5342 </conditional>
5343 <conditional name="CONDITIONAL_to">
5344 <param name="CONDITIONAL_SELECT_to" type="select" label="Set To" help="" argument="--to">
5345 <option value="no_set" selected="True">Don't set</option>
5346 <option value="set">Set value(s)</option>
5347 </param>
5348 <when value="no_set">
5349 </when>
5350 <when value="set">
5351
5352 <param name="to_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/>
5353 </when>
5354 </conditional>
5355 <conditional name="CONDITIONAL_snp">
5356 <param name="CONDITIONAL_SELECT_snp" type="select" label="Set Snp" help="Specify a single variant to load. " argument="--snp">
5357 <option value="no_set" selected="True">Don't set</option>
5358 <option value="set">Set value(s)</option>
5359 </param>
5360 <when value="no_set">
5361 </when>
5362 <when value="set">
5363
5364 <param name="snp_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/>
5365 </when>
5366 </conditional>
5367 <conditional name="CONDITIONAL_exclude_snp">
5368 <param name="CONDITIONAL_SELECT_exclude_snp" type="select" label="Set Exclude snp" help="Specify a single variant to exclude. " argument="--exclude-snp">
5369 <option value="no_set" selected="True">Don't set</option>
5370 <option value="set">Set value(s)</option>
5371 </param>
5372 <when value="no_set">
5373 </when>
5374 <when value="set">
5375
5376 <param name="exclude_snp_MOD_0_0" type="text" label="ID" value="" optional="True" argument="ID" help=""/>
5377 </when>
5378 </conditional>
5379 <conditional name="CONDITIONAL_window">
5380 <param name="CONDITIONAL_SELECT_window" type="select" label="Set Window" help="With --snp/--exclude-snp, loads/excludes all variants within half the specified kb distance of the named one. " argument="--window">
5381 <option value="no_set" selected="True">Don't set</option>
5382 <option value="set">Set value(s)</option>
5383 </param>
5384 <when value="no_set">
5385 </when>
5386 <when value="set">
5387
5388 <param name="window_MOD_0_0" type="text" label="kbs" value="" optional="True" argument="kbs" help=""/>
5389 </when>
5390 </conditional>
5391 <conditional name="CONDITIONAL_from_bp">
5392 <param name="CONDITIONAL_SELECT_from_bp" type="select" label="Set From bp" help="Use base-pair coordinates to define a variant range to " argument="--from-bp">
5393 <option value="no_set" selected="True">Don't set</option>
5394 <option value="set">Set value(s)</option>
5395 </param>
5396 <when value="no_set">
5397 </when>
5398 <when value="set">
5399
5400 <param name="from_bp_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
5401 </when>
5402 </conditional>
5403 <conditional name="CONDITIONAL_to_bp">
5404 <param name="CONDITIONAL_SELECT_to_bp" type="select" label="Set To bp" help="" argument="--to-bp">
5405 <option value="no_set" selected="True">Don't set</option>
5406 <option value="set">Set value(s)</option>
5407 </param>
5408 <when value="no_set">
5409 </when>
5410 <when value="set">
5411
5412 <param name="to_bp_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
5413 </when>
5414 </conditional>
5415 <conditional name="CONDITIONAL_from_kb">
5416 <param name="CONDITIONAL_SELECT_from_kb" type="select" label="Set From kb" help="" argument="--from-kb">
5417 <option value="no_set" selected="True">Don't set</option>
5418 <option value="set">Set value(s)</option>
5419 </param>
5420 <when value="no_set">
5421 </when>
5422 <when value="set">
5423
5424 <param name="from_kb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
5425 </when>
5426 </conditional>
5427 <conditional name="CONDITIONAL_to_kb">
5428 <param name="CONDITIONAL_SELECT_to_kb" type="select" label="Set To kb" help="" argument="--to-kb">
5429 <option value="no_set" selected="True">Don't set</option>
5430 <option value="set">Set value(s)</option>
5431 </param>
5432 <when value="no_set">
5433 </when>
5434 <when value="set">
5435
5436 <param name="to_kb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
5437 </when>
5438 </conditional>
5439 <conditional name="CONDITIONAL_from_mb">
5440 <param name="CONDITIONAL_SELECT_from_mb" type="select" label="Set From mb" help="" argument="--from-mb">
5441 <option value="no_set" selected="True">Don't set</option>
5442 <option value="set">Set value(s)</option>
5443 </param>
5444 <when value="no_set">
5445 </when>
5446 <when value="set">
5447
5448 <param name="from_mb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
5449 </when>
5450 </conditional>
5451 <conditional name="CONDITIONAL_to_mb">
5452 <param name="CONDITIONAL_SELECT_to_mb" type="select" label="Set To mb" help="" argument="--to-mb">
5453 <option value="no_set" selected="True">Don't set</option>
5454 <option value="set">Set value(s)</option>
5455 </param>
5456 <when value="no_set">
5457 </when>
5458 <when value="set">
5459
5460 <param name="to_mb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
5461 </when>
5462 </conditional>
5463 <conditional name="CONDITIONAL_snps">
5464 <param name="CONDITIONAL_SELECT_snps" type="select" label="Set Snps" help="Use IDs to specify variant range(s) to load or " argument="--snps">
5465 <option value="no_set" selected="True">Don't set</option>
5466 <option value="set">Set value(s)</option>
5467 </param>
5468 <when value="no_set">
5469 </when>
5470 <when value="set">
5471
5472 <param name="snps_MOD_0_0" type="text" label="var IDs..." value="" optional="True" argument="var IDs..." help="Multiple values are allowed"/>
5473 </when>
5474 </conditional>
5475 <conditional name="CONDITIONAL_exclude_snps">
5476 <param name="CONDITIONAL_SELECT_exclude_snps" type="select" label="Set Exclude snps" help="" argument="--exclude-snps">
5477 <option value="no_set" selected="True">Don't set</option>
5478 <option value="set">Set value(s)</option>
5479 </param>
5480 <when value="no_set">
5481 </when>
5482 <when value="set">
5483
5484 <param name="exclude_snps_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
5485 </when>
5486 </conditional>
5487 <conditional name="CONDITIONAL_force_intersect">
5488 <param name="CONDITIONAL_SELECT_force_intersect" type="select" label="Set Force intersect" help="PLINK 2 normally errors out when multiple variant inclusion filters (--extract, --extract-col-cond, --extract-intersect, --from/--to, --from-bp/--to-bp, --snp, --snps) are specified. --force-intersect allows the run to proceed; the set intersection will be taken. " argument="--force-intersect">
5489 <option value="no_set" selected="True">Don't set</option>
5490 <option value="set">Set value(s)</option>
5491 </param>
5492 <when value="no_set">
5493 </when>
5494 <when value="set">
5495
5496 </when>
5497 </conditional>
5498 <conditional name="CONDITIONAL_thin">
5499 <param name="CONDITIONAL_SELECT_thin" type="select" label="Set Thin" help="Randomly remove variants, retaining each with prob. p. " argument="--thin">
5500 <option value="no_set" selected="True">Don't set</option>
5501 <option value="set">Set value(s)</option>
5502 </param>
5503 <when value="no_set">
5504 </when>
5505 <when value="set">
5506
5507 <param name="thin_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/>
5508 </when>
5509 </conditional>
5510 <conditional name="CONDITIONAL_thin_count">
5511 <param name="CONDITIONAL_SELECT_thin_count" type="select" label="Set Thin count" help="Randomly remove variants until n of them remain. " argument="--thin-count">
5512 <option value="no_set" selected="True">Don't set</option>
5513 <option value="set">Set value(s)</option>
5514 </param>
5515 <when value="no_set">
5516 </when>
5517 <when value="set">
5518
5519 <param name="thin_count_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/>
5520 </when>
5521 </conditional>
5522 <conditional name="CONDITIONAL_bp_space">
5523 <param name="CONDITIONAL_SELECT_bp_space" type="select" label="Set Bp space" help="Remove variants so that each pair is no closer than the given bp distance. " argument="--bp-space">
5524 <option value="no_set" selected="True">Don't set</option>
5525 <option value="set">Set value(s)</option>
5526 </param>
5527 <when value="no_set">
5528 </when>
5529 <when value="set">
5530
5531 <param name="bp_space_MOD_0_0" type="text" label="bps" value="" optional="True" argument="bps" help=""/>
5532 </when>
5533 </conditional>
5534 <conditional name="CONDITIONAL_thin_indiv">
5535 <param name="CONDITIONAL_SELECT_thin_indiv" type="select" label="Set Thin indiv" help="Randomly remove samples, retaining with prob. p. " argument="--thin-indiv">
5536 <option value="no_set" selected="True">Don't set</option>
5537 <option value="set">Set value(s)</option>
5538 </param>
5539 <when value="no_set">
5540 </when>
5541 <when value="set">
5542
5543 <param name="thin_indiv_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/>
5544 </when>
5545 </conditional>
5546 <conditional name="CONDITIONAL_thin_indiv_count">
5547 <param name="CONDITIONAL_SELECT_thin_indiv_count" type="select" label="Set Thin indiv count" help="Randomly remove samples until n of them remain. " argument="--thin-indiv-count">
5548 <option value="no_set" selected="True">Don't set</option>
5549 <option value="set">Set value(s)</option>
5550 </param>
5551 <when value="no_set">
5552 </when>
5553 <when value="set">
5554
5555 <param name="thin_indiv_count_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/>
5556 </when>
5557 </conditional>
5558 <conditional name="CONDITIONAL_keep_col_match">
5559 <param name="CONDITIONAL_SELECT_keep_col_match" type="select" label="Set Keep col match" help="Exclude all samples without a 3rd column entry in the given file exactly matching one of the given strings. (Separate multiple strings with spaces.) " argument="--keep-col-match">
5560 <option value="no_set" selected="True">Don't set</option>
5561 <option value="set">Set value(s)</option>
5562 </param>
5563 <when value="no_set">
5564 </when>
5565 <when value="set">
5566
5567 <param name="keep_col_match_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
5568 <param name="keep_col_match_MOD_1_0" type="text" label="val(s)..." value="" optional="True" argument="val(s)..." help="Multiple values are allowed"/>
5569 </when>
5570 </conditional>
5571 <conditional name="CONDITIONAL_keep_col_match_name">
5572 <param name="CONDITIONAL_SELECT_keep_col_match_name" type="select" label="Set Keep col match name" help="Check column with given name instead. " argument="--keep-col-match-name">
5573 <option value="no_set" selected="True">Don't set</option>
5574 <option value="set">Set value(s)</option>
5575 </param>
5576 <when value="no_set">
5577 </when>
5578 <when value="set">
5579
5580 <param name="keep_col_match_name_MOD_0_0" type="text" label="col name" value="" optional="True" argument="col name" help=""/>
5581 </when>
5582 </conditional>
5583 <conditional name="CONDITIONAL_keep_col_match_num">
5584 <param name="CONDITIONAL_SELECT_keep_col_match_num" type="select" label="Set Keep col match num" help="Check nth column instead. " argument="--keep-col-match-num">
5585 <option value="no_set" selected="True">Don't set</option>
5586 <option value="set">Set value(s)</option>
5587 </param>
5588 <when value="no_set">
5589 </when>
5590 <when value="set">
5591
5592 <param name="keep_col_match_num_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/>
5593 </when>
5594 </conditional>
5595 <conditional name="CONDITIONAL_geno">
5596 <param name="CONDITIONAL_SELECT_geno" type="select" label="Set Geno" help="" argument="--geno">
5597 <option value="no_set" selected="True">Don't set</option>
5598 <option value="set">Set value(s)</option>
5599 </param>
5600 <when value="no_set">
5601 </when>
5602 <when value="set">
5603
5604 <param name="geno_MOD_0_0" type="text" label="val" value="" optional="False" argument="val" help=""/>
5605 <conditional name="CONDITIONAL_geno_MOD_1">
5606 <param name="CONDITIONAL_SELECT_geno_MOD_1" type="select" label="How to set Geno">
5607 <option value="no_set" selected="True">Don't set</option>
5608 <option value="from_list">Select from list</option>
5609
5610 </param>
5611 <when value="no_set">
5612 </when>
5613
5614 <when value="from_list">
5615 <param name="geno_MOD_1" type="select" label="Select value">
5616 <option value="{dosage">{dosage</option>
5617 <option value="hh-missing}">hh-missing}</option>
5618 </param>
5619 </when>
5620 </conditional>
5621 </when>
5622 </conditional>
5623 <conditional name="CONDITIONAL_mind">
5624 <param name="CONDITIONAL_SELECT_mind" type="select" label="Set Mind" help="Exclude variants (--geno) and/or samples (--mind) with missing call frequencies greater than a threshold (default 0.1). (Note that the default threshold is only applied if --geno/--mind is invoked without a parameter; when --geno/--mind is not invoked, no missing call frequency ceiling is enforced at all. Other inclusion/exclusion default thresholds work the same way.) By default, when a dosage is present but a hardcall is not, the genotype is treated as missing; add the 'dosage' modifier to treat this case as nonmissing. Alternatively, you can use 'hh-missing' to also treat heterozygous haploid calls as missing." argument="--mind">
5625 <option value="no_set" selected="True">Don't set</option>
5626 <option value="set">Set value(s)</option>
5627 </param>
5628 <when value="no_set">
5629 </when>
5630 <when value="set">
5631
5632 <param name="mind_MOD_0_0" type="text" label="val" value="" optional="False" argument="val" help=""/>
5633 <conditional name="CONDITIONAL_mind_MOD_1">
5634 <param name="CONDITIONAL_SELECT_mind_MOD_1" type="select" label="How to set Mind">
5635 <option value="no_set" selected="True">Don't set</option>
5636 <option value="from_list">Select from list</option>
5637
5638 </param>
5639 <when value="no_set">
5640 </when>
5641
5642 <when value="from_list">
5643 <param name="mind_MOD_1" type="select" label="Select value">
5644 <option value="{dosage">{dosage</option>
5645 <option value="hh-missing}">hh-missing}</option>
5646 </param>
5647 </when>
5648 </conditional>
5649 </when>
5650 </conditional>
5651 <conditional name="CONDITIONAL_require_pheno">
5652 <param name="CONDITIONAL_SELECT_require_pheno" type="select" label="Set Require pheno" help="Remove samples missing any of the named " argument="--require-pheno">
5653 <option value="no_set" selected="True">Don't set</option>
5654 <option value="set">Set value(s)</option>
5655 </param>
5656 <when value="no_set">
5657 </when>
5658 <when value="set">
5659
5660 <param name="require_pheno_MOD_0_0" type="text" label="name(s)..." value="" optional="False" argument="name(s)..." help="Multiple values are allowed"/>
5661 </when>
5662 </conditional>
5663 <conditional name="CONDITIONAL_require_covar">
5664 <param name="CONDITIONAL_SELECT_require_covar" type="select" label="Set Require covar" help="" argument="--require-covar">
5665 <option value="no_set" selected="True">Don't set</option>
5666 <option value="set">Set value(s)</option>
5667 </param>
5668 <when value="no_set">
5669 </when>
5670 <when value="set">
5671
5672 <param name="require_covar_MOD_0_0" type="text" label="name(s)..." value="" optional="False" argument="name(s)..." help="Multiple values are allowed"/>
5673 </when>
5674 </conditional>
5675 <conditional name="CONDITIONAL_maf">
5676 <param name="CONDITIONAL_SELECT_maf" type="select" label="Set Maf" help="Exclude variants with allele frequency lower than a (alias: --min-af) threshold (default 0.01). By default, the nonmajor allele frequency is used; the other supported modes are 'nref' (non-reference), 'alt1', and 'minor' (least frequent). bcftools freq:mode notation is permitted." argument="--maf">
5677 <option value="no_set" selected="True">Don't set</option>
5678 <option value="set">Set value(s)</option>
5679 </param>
5680 <when value="no_set">
5681 </when>
5682 <when value="set">
5683
5684 <param name="maf_MOD_0_0" type="float" label="freq" value="" optional="False" argument="freq" help=""/>
5685 <param name="maf_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
5686 </when>
5687 </conditional>
5688 <conditional name="CONDITIONAL_max_maf">
5689 <param name="CONDITIONAL_SELECT_max_maf" type="select" label="Set Max maf" help="Exclude variants with MAF greater than the (alias: --max-af) threshold." argument="--max-maf">
5690 <option value="no_set" selected="True">Don't set</option>
5691 <option value="set">Set value(s)</option>
5692 </param>
5693 <when value="no_set">
5694 </when>
5695 <when value="set">
5696
5697 <param name="max_maf_MOD_0_0" type="float" label="freq" value="" optional="True" argument="freq" help=""/>
5698 <param name="max_maf_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
5699 </when>
5700 </conditional>
5701 <conditional name="CONDITIONAL_mac">
5702 <param name="CONDITIONAL_SELECT_mac" type="select" label="Set Mac" help="Exclude variants with allele dosage lower than the (alias: --min-ac) given threshold." argument="--mac">
5703 <option value="no_set" selected="True">Don't set</option>
5704 <option value="set">Set value(s)</option>
5705 </param>
5706 <when value="no_set">
5707 </when>
5708 <when value="set">
5709
5710 <param name="mac_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/>
5711 <param name="mac_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
5712 </when>
5713 </conditional>
5714 <conditional name="CONDITIONAL_max_mac">
5715 <param name="CONDITIONAL_SELECT_max_mac" type="select" label="Set Max mac" help="Exclude variants with allele dosage greater than (alias: --max-ac) the given threshold." argument="--max-mac">
5716 <option value="no_set" selected="True">Don't set</option>
5717 <option value="set">Set value(s)</option>
5718 </param>
5719 <when value="no_set">
5720 </when>
5721 <when value="set">
5722
5723 <param name="max_mac_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/>
5724 <param name="max_mac_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
5725 </when>
5726 </conditional>
5727 <conditional name="CONDITIONAL_maf_succ">
5728 <param name="CONDITIONAL_SELECT_maf_succ" type="select" label="Set Maf succ" help="Rule of succession allele frequency estimation (used in EIGENSOFT). Given j observations of one allele and k observations of the other for a biallelic variant, infer allele frequencies of (j+1) / (j+k+2) and (k+1) / (j+k+2), rather than the default j / (j+k) and k / (j+k). Note that this does not affect --freq's output. " argument="--maf-succ">
5729 <option value="no_set" selected="True">Don't set</option>
5730 <option value="set">Set value(s)</option>
5731 </param>
5732 <when value="no_set">
5733 </when>
5734 <when value="set">
5735
5736 </when>
5737 </conditional>
5738 <conditional name="CONDITIONAL_min_alleles">
5739 <param name="CONDITIONAL_SELECT_min_alleles" type="select" label="Set Min alleles" help="Exclude variants with fewer than the given # of alleles. (When a variant has exactly one ALT allele, and it's a missing-code, it's excluded by &quot;--min-alleles 2&quot;.) " argument="--min-alleles">
5740 <option value="no_set" selected="True">Don't set</option>
5741 <option value="set">Set value(s)</option>
5742 </param>
5743 <when value="no_set">
5744 </when>
5745 <when value="set">
5746
5747 <param name="min_alleles_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/>
5748 </when>
5749 </conditional>
5750 <conditional name="CONDITIONAL_max_alleles">
5751 <param name="CONDITIONAL_SELECT_max_alleles" type="select" label="Set Max alleles" help="Exclude variants with more than the given # of alleles. " argument="--max-alleles">
5752 <option value="no_set" selected="True">Don't set</option>
5753 <option value="set">Set value(s)</option>
5754 </param>
5755 <when value="no_set">
5756 </when>
5757 <when value="set">
5758
5759 <param name="max_alleles_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/>
5760 </when>
5761 </conditional>
5762 <conditional name="CONDITIONAL_read_freq">
5763 <param name="CONDITIONAL_SELECT_read_freq" type="select" label="Set Read freq" help="Load allele frequency estimates from the given --freq or --geno-counts (or PLINK 1.9 --freqx) report, instead of imputing them from the immediate dataset. " argument="--read-freq">
5764 <option value="no_set" selected="True">Don't set</option>
5765 <option value="set">Set value(s)</option>
5766 </param>
5767 <when value="no_set">
5768 </when>
5769 <when value="set">
5770
5771 <param name="read_freq_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/>
5772 </when>
5773 </conditional>
5774 <conditional name="CONDITIONAL_hwe">
5775 <param name="CONDITIONAL_SELECT_hwe" type="select" label="Set Hwe" help="Exclude variants with Hardy-Weinberg equilibrium exact test p-values below a threshold. * By default, only founders are considered. * chrX p-values are now computed using Graffelman and Weir's method. * For variants with k alleles with k&gt;2, k separate 'biallelic' tests are performed, and the variant is filtered out if any of them fail. * With 'keep-fewhet', variants which fail the test in the too-few-hets direction are not excluded. On chrX, this uses the ratio between the Graffelman/Weir p-value and the female-only p-value. * There is currently no special handling of case/control phenotypes." argument="--hwe">
5776 <option value="no_set" selected="True">Don't set</option>
5777 <option value="set">Set value(s)</option>
5778 </param>
5779 <when value="no_set">
5780 </when>
5781 <when value="set">
5782
5783 <param name="hwe_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/>
5784 <param name="hwe_MOD_1_0" type="text" label="'midp'" value="" optional="False" argument="'midp'" help=""/>
5785 <param name="hwe_MOD_2_0" type="text" label="'keep-fewhet'" value="" optional="False" argument="'keep-fewhet'" help=""/>
5786 </when>
5787 </conditional>
5788 <conditional name="CONDITIONAL_mach_r2_filter">
5789 <param name="CONDITIONAL_SELECT_mach_r2_filter" type="select" label="Set Mach r2 filter" help="Exclude variants with MaCH imputation quality metric less than min or greater than max (defaults 0.1 and 2.0). (Monomorphic variants, with r2 = nan, are not excluded.) * This is NOT identical to the R2 metric reported by Minimac3 0.1.13+; see below. * If a single parameter is provided, it is treated as the minimum. * The metric is not computed on chrX and MT. " argument="--mach-r2-filter">
5790 <option value="no_set" selected="True">Don't set</option>
5791 <option value="set">Set value(s)</option>
5792 </param>
5793 <when value="no_set">
5794 </when>
5795 <when value="set">
5796
5797 <param name="mach_r2_filter_MOD_0_0" type="text" label="min" value="" optional="False" argument="min" help=""/>
5798 <param name="mach_r2_filter_MOD_1_0" type="text" label="max" value="" optional="False" argument="max" help=""/>
5799 </when>
5800 </conditional>
5801 <conditional name="CONDITIONAL_minimac3_r2_filter">
5802 <param name="CONDITIONAL_SELECT_minimac3_r2_filter" type="select" label="Set Minimac3 r2 filter" help="Compute Minimac3 R2 values from scratch, and exclude variants with R2 less than min or (if max is provided) greater than max. * Note that this requires phased-dosage data for all samples and variants; otherwise this will systematically underestimate imputation quality, since unphased hardcalls/dosages are treated as if they were maximally uncertain. (Use --extract-if-info/--exclude-if-info to filter on precomputed Minimac3 R2 in a VCF/.pvar INFO column.) " argument="--minimac3-r2-filter">
5803 <option value="no_set" selected="True">Don't set</option>
5804 <option value="set">Set value(s)</option>
5805 </param>
5806 <when value="no_set">
5807 </when>
5808 <when value="set">
5809
5810 <param name="minimac3_r2_filter_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/>
5811 <param name="minimac3_r2_filter_MOD_1_0" type="text" label="max" value="" optional="False" argument="max" help=""/>
5812 </when>
5813 </conditional>
5814 <conditional name="CONDITIONAL_keep_females">
5815 <param name="CONDITIONAL_SELECT_keep_females" type="select" label="Set Keep females" help="Exclude male and unknown-sex samples. " argument="--keep-females">
5816 <option value="no_set" selected="True">Don't set</option>
5817 <option value="set">Set value(s)</option>
5818 </param>
5819 <when value="no_set">
5820 </when>
5821 <when value="set">
5822
5823 </when>
5824 </conditional>
5825 <conditional name="CONDITIONAL_keep_males">
5826 <param name="CONDITIONAL_SELECT_keep_males" type="select" label="Set Keep males" help="Exclude female and unknown-sex samples. " argument="--keep-males">
5827 <option value="no_set" selected="True">Don't set</option>
5828 <option value="set">Set value(s)</option>
5829 </param>
5830 <when value="no_set">
5831 </when>
5832 <when value="set">
5833
5834 </when>
5835 </conditional>
5836 <conditional name="CONDITIONAL_keep_nosex">
5837 <param name="CONDITIONAL_SELECT_keep_nosex" type="select" label="Set Keep nosex" help="Exclude all known-sex samples. " argument="--keep-nosex">
5838 <option value="no_set" selected="True">Don't set</option>
5839 <option value="set">Set value(s)</option>
5840 </param>
5841 <when value="no_set">
5842 </when>
5843 <when value="set">
5844
5845 </when>
5846 </conditional>
5847 <conditional name="CONDITIONAL_remove_females">
5848 <param name="CONDITIONAL_SELECT_remove_females" type="select" label="Set Remove females" help="Exclude female samples. " argument="--remove-females">
5849 <option value="no_set" selected="True">Don't set</option>
5850 <option value="set">Set value(s)</option>
5851 </param>
5852 <when value="no_set">
5853 </when>
5854 <when value="set">
5855
5856 </when>
5857 </conditional>
5858 <conditional name="CONDITIONAL_remove_males">
5859 <param name="CONDITIONAL_SELECT_remove_males" type="select" label="Set Remove males" help="Exclude male samples. " argument="--remove-males">
5860 <option value="no_set" selected="True">Don't set</option>
5861 <option value="set">Set value(s)</option>
5862 </param>
5863 <when value="no_set">
5864 </when>
5865 <when value="set">
5866
5867 </when>
5868 </conditional>
5869 <conditional name="CONDITIONAL_remove_nosex">
5870 <param name="CONDITIONAL_SELECT_remove_nosex" type="select" label="Set Remove nosex" help="Exclude unknown-sex samples. " argument="--remove-nosex">
5871 <option value="no_set" selected="True">Don't set</option>
5872 <option value="set">Set value(s)</option>
5873 </param>
5874 <when value="no_set">
5875 </when>
5876 <when value="set">
5877
5878 </when>
5879 </conditional>
5880 <conditional name="CONDITIONAL_keep_founders">
5881 <param name="CONDITIONAL_SELECT_keep_founders" type="select" label="Set Keep founders" help="Exclude nonfounder samples. " argument="--keep-founders">
5882 <option value="no_set" selected="True">Don't set</option>
5883 <option value="set">Set value(s)</option>
5884 </param>
5885 <when value="no_set">
5886 </when>
5887 <when value="set">
5888
5889 </when>
5890 </conditional>
5891 <conditional name="CONDITIONAL_keep_nonfounders">
5892 <param name="CONDITIONAL_SELECT_keep_nonfounders" type="select" label="Set Keep nonfounders" help="Exclude founder samples. " argument="--keep-nonfounders">
5893 <option value="no_set" selected="True">Don't set</option>
5894 <option value="set">Set value(s)</option>
5895 </param>
5896 <when value="no_set">
5897 </when>
5898 <when value="set">
5899
5900 </when>
5901 </conditional>
5902 <conditional name="CONDITIONAL_keep_if">
5903 <param name="CONDITIONAL_SELECT_keep_if" type="select" label="Set Keep if" help="Exclude samples which don't/do satisfy a " argument="--keep-if">
5904 <option value="no_set" selected="True">Don't set</option>
5905 <option value="set">Set value(s)</option>
5906 </param>
5907 <when value="no_set">
5908 </when>
5909 <when value="set">
5910
5911 <param name="keep_if_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/>
5912 <param name="keep_if_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/>
5913 <param name="keep_if_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
5914 </when>
5915 </conditional>
5916 <conditional name="CONDITIONAL_remove_if">
5917 <param name="CONDITIONAL_SELECT_remove_if" type="select" label="Set Remove if" help="" argument="--remove-if">
5918 <option value="no_set" selected="True">Don't set</option>
5919 <option value="set">Set value(s)</option>
5920 </param>
5921 <when value="no_set">
5922 </when>
5923 <when value="set">
5924
5925 <param name="remove_if_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/>
5926 <param name="remove_if_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/>
5927 <param name="remove_if_MOD_2_0" type="text" label="v" value="" optional="True" argument="v" help=""/>
5928 </when>
5929 </conditional>
5930 <conditional name="CONDITIONAL_nonfounders">
5931 <param name="CONDITIONAL_SELECT_nonfounders" type="select" label="Set Nonfounders" help="Include nonfounders in allele freq/HWE calculations. " argument="--nonfounders">
5932 <option value="no_set" selected="True">Don't set</option>
5933 <option value="set">Set value(s)</option>
5934 </param>
5935 <when value="no_set">
5936 </when>
5937 <when value="set">
5938
5939 </when>
5940 </conditional>
5941 <conditional name="CONDITIONAL_bad_freqs">
5942 <param name="CONDITIONAL_SELECT_bad_freqs" type="select" label="Set Bad freqs" help="When PLINK 2 needs decent allele frequencies, it normally errors out if they aren't provided by --read-freq and less than 50 founders are available to impute them from. Use --bad-freqs to force PLINK 2 to proceed in this case. " argument="--bad-freqs">
5943 <option value="no_set" selected="True">Don't set</option>
5944 <option value="set">Set value(s)</option>
5945 </param>
5946 <when value="no_set">
5947 </when>
5948 <when value="set">
5949
5950 </when>
5951 </conditional>
5952 <conditional name="CONDITIONAL_export_allele">
5953 <param name="CONDITIONAL_SELECT_export_allele" type="select" label="Set Export allele" help="With --export A/A-transpose/AD, count alleles named in the file, instead of REF alleles. " argument="--export-allele">
5954 <option value="no_set" selected="True">Don't set</option>
5955 <option value="set">Set value(s)</option>
5956 </param>
5957 <when value="no_set">
5958 </when>
5959 <when value="set">
5960
5961 <param name="export_allele_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/>
5962 </when>
5963 </conditional>
5964 <conditional name="CONDITIONAL_output_chr">
5965 <param name="CONDITIONAL_SELECT_output_chr" type="select" label="Set Output chr" help="Set chromosome coding scheme in output files by providing the desired human mitochondrial code. Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM', and 'chrMT'; default is now 'MT' (note that this is a change from PLINK 1.x, which defaulted to '26'). " argument="--output-chr">
5966 <option value="no_set" selected="True">Don't set</option>
5967 <option value="set">Set value(s)</option>
5968 </param>
5969 <when value="no_set">
5970 </when>
5971 <when value="set">
5972
5973 <param name="output_chr_MOD_0_0" type="text" label="MT code" value="" optional="True" argument="MT code" help=""/>
5974 </when>
5975 </conditional>
5976 <conditional name="CONDITIONAL_output_missing_genotype">
5977 <param name="CONDITIONAL_SELECT_output_missing_genotype" type="select" label="Set Output missing genotype" help="Set the code used to represent missing genotypes in output files (default '.'). " argument="--output-missing-genotype">
5978 <option value="no_set" selected="True">Don't set</option>
5979 <option value="set">Set value(s)</option>
5980 </param>
5981 <when value="no_set">
5982 </when>
5983 <when value="set">
5984
5985 <param name="output_missing_genotype_MOD_0_0" type="text" label="ch" value="" optional="True" argument="ch" help=""/>
5986 </when>
5987 </conditional>
5988 <conditional name="CONDITIONAL_output_missing_phenotype">
5989 <param name="CONDITIONAL_SELECT_output_missing_phenotype" type="select" label="Set Output missing phenotype" help="Set the string used to represent missing phenotypes in output files (default 'NA'). " argument="--output-missing-phenotype">
5990 <option value="no_set" selected="True">Don't set</option>
5991 <option value="set">Set value(s)</option>
5992 </param>
5993 <when value="no_set">
5994 </when>
5995 <when value="set">
5996
5997 <param name="output_missing_phenotype_MOD_0_0" type="text" label="s" value="" optional="True" argument="s" help=""/>
5998 </when>
5999 </conditional>
6000 <conditional name="CONDITIONAL_sort_vars">
6001 <param name="CONDITIONAL_SELECT_sort_vars" type="select" label="Set Sort vars" help="Sort variants by chromosome, then position, then ID. The following string orders are supported: * 'natural'/'n': Natural sort (default). * 'ascii'/'a': ASCII. This must be used with --make-[b]pgen/--make-bed. " argument="--sort-vars">
6002 <option value="no_set" selected="True">Don't set</option>
6003 <option value="set">Set value(s)</option>
6004 </param>
6005 <when value="no_set">
6006 </when>
6007 <when value="set">
6008
6009 <param name="sort_vars_MOD_0_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
6010 </when>
6011 </conditional>
6012 <conditional name="CONDITIONAL_set_hh_missing">
6013 <param name="CONDITIONAL_SELECT_set_hh_missing" type="select" label="Set Set hh missing" help="Make --make-[b]pgen/--make-bed set non-MT heterozygous haploid hardcalls, and all female chrY calls, to missing. (Unlike PLINK 1.x, this treats unknown-sex chrY genotypes like males, not females.) By default, all associated dosages are also erased; use 'keep-dosage' to keep them all. " argument="--set-hh-missing">
6014 <option value="no_set" selected="True">Don't set</option>
6015 <option value="set">Set value(s)</option>
6016 </param>
6017 <when value="no_set">
6018 </when>
6019 <when value="set">
6020
6021 <param name="set_hh_missing_MOD_0_0" type="text" label="'keep-dosage'" value="" optional="False" argument="'keep-dosage'" help=""/>
6022 </when>
6023 </conditional>
6024 <conditional name="CONDITIONAL_set_mixed_mt_missing">
6025 <param name="CONDITIONAL_SELECT_set_mixed_mt_missing" type="select" label="Set Set mixed mt missing" help="Make --make-[b]pgen/--make-bed set mixed MT hardcalls to missing. " argument="--set-mixed-mt-missing">
6026 <option value="no_set" selected="True">Don't set</option>
6027 <option value="set">Set value(s)</option>
6028 </param>
6029 <when value="no_set">
6030 </when>
6031 <when value="set">
6032
6033 <param name="set_mixed_mt_missing_MOD_0_0" type="text" label="'keep-dosage'" value="" optional="False" argument="'keep-dosage'" help=""/>
6034 </when>
6035 </conditional>
6036 <conditional name="CONDITIONAL_OVERLOADED_split_par">
6037 <param name="CONDITIONAL_OVERLOADED_SELECT_split_par" type="select" label="Choose argument form for Split_par" help="Overloaded argument, must chose a form">
6038 <option value="form_0">Form 0</option>
6039 <option value="form_1">Form 1</option>
6040 </param>
6041 <when value="form_0">
6042
6043 <conditional name="CONDITIONAL_split_par">
6044 <param name="CONDITIONAL_SELECT_split_par" type="select" label="Set Split par" help="Changes chromosome code of all X chromosome " argument="--split-par">
6045 <option value="no_set" selected="True">Don't set</option>
6046 <option value="set">Set value(s)</option>
6047 </param>
6048 <when value="no_set">
6049 </when>
6050 <when value="set">
6051
6052 <param name="split_par_MOD_0_0" type="text" label="bp1" value="" optional="True" argument="bp1" help=""/>
6053 <param name="split_par_MOD_1_0" type="text" label="bp2" value="" optional="True" argument="bp2" help=""/>
6054 </when>
6055 </conditional>
6056 </when>
6057 <when value="form_1">
6058
6059 <conditional name="CONDITIONAL_split_par">
6060 <param name="CONDITIONAL_SELECT_split_par" type="select" label="Set Split par" help="* 'b36'/'hg18' = NCBI 36, 2709521/154584237 * 'b37'/'hg19' = GRCh37, 2699520/154931044 * 'b38'/'hg38' = GRCh38, 2781479/155701383 " argument="--split-par">
6061 <option value="no_set" selected="True">Don't set</option>
6062 <option value="set">Set value(s)</option>
6063 </param>
6064 <when value="no_set">
6065 </when>
6066 <when value="set">
6067
6068 <param name="split_par_MOD_0_0" type="text" label="build" value="" optional="True" argument="build" help=""/>
6069 <param name="split_par_MOD_1_0" type="text" label="= bp1 to PAR1, and those with position" value="" optional="True" argument="= bp1 to PAR1, and those with position" help=""/>
6070 </when>
6071 </conditional>
6072 </when>
6073 </conditional>
6074 <conditional name="CONDITIONAL_merge_par">
6075 <param name="CONDITIONAL_SELECT_merge_par" type="select" label="Set Merge par" help='Merge PAR1/PAR2 back with X. Requires PAR1 to be positioned immediately before X, and PAR2 to be immediately after X. (Should *not* be used with "--export vcf", since it causes male homozygous/missing calls in PAR1/PAR2 to be reported as haploid.) ' argument="--merge-par">
6076 <option value="no_set" selected="True">Don't set</option>
6077 <option value="set">Set value(s)</option>
6078 </param>
6079 <when value="no_set">
6080 </when>
6081 <when value="set">
6082
6083 </when>
6084 </conditional>
6085 <conditional name="CONDITIONAL_merge_x">
6086 <param name="CONDITIONAL_SELECT_merge_x" type="select" label="Set Merge x" help="Merge XY back with X. This usually has to be combined with --sort-vars. " argument="--merge-x">
6087 <option value="no_set" selected="True">Don't set</option>
6088 <option value="set">Set value(s)</option>
6089 </param>
6090 <when value="no_set">
6091 </when>
6092 <when value="set">
6093
6094 </when>
6095 </conditional>
6096 <conditional name="CONDITIONAL_set_missing_var_ids">
6097 <param name="CONDITIONAL_SELECT_set_missing_var_ids" type="select" label="Set Set missing var ids" help="Given a template string with a '@' where the " argument="--set-missing-var-ids">
6098 <option value="no_set" selected="True">Don't set</option>
6099 <option value="set">Set value(s)</option>
6100 </param>
6101 <when value="no_set">
6102 </when>
6103 <when value="set">
6104
6105 <param name="set_missing_var_ids_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/>
6106 </when>
6107 </conditional>
6108 <conditional name="CONDITIONAL_set_all_var_ids">
6109 <param name="CONDITIONAL_SELECT_set_all_var_ids" type="select" label="Set Set all var ids" help="" argument="--set-all-var-ids">
6110 <option value="no_set" selected="True">Don't set</option>
6111 <option value="set">Set value(s)</option>
6112 </param>
6113 <when value="no_set">
6114 </when>
6115 <when value="set">
6116
6117 <param name="set_all_var_ids_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/>
6118 </when>
6119 </conditional>
6120 <conditional name="CONDITIONAL_var_id_multi">
6121 <param name="CONDITIONAL_SELECT_var_id_multi" type="select" label="Set Var id multi" help="Specify alternative templates for multiallelic " argument="--var-id-multi">
6122 <option value="no_set" selected="True">Don't set</option>
6123 <option value="set">Set value(s)</option>
6124 </param>
6125 <when value="no_set">
6126 </when>
6127 <when value="set">
6128
6129 <param name="var_id_multi_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/>
6130 </when>
6131 </conditional>
6132 <conditional name="CONDITIONAL_var_id_multi_nonsnp">
6133 <param name="CONDITIONAL_SELECT_var_id_multi_nonsnp" type="select" label="Set Var id multi nonsnp" help="" argument="--var-id-multi-nonsnp">
6134 <option value="no_set" selected="True">Don't set</option>
6135 <option value="set">Set value(s)</option>
6136 </param>
6137 <when value="no_set">
6138 </when>
6139 <when value="set">
6140
6141 <param name="var_id_multi_nonsnp_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/>
6142 </when>
6143 </conditional>
6144 <conditional name="CONDITIONAL_new_id_max_allele_len">
6145 <param name="CONDITIONAL_SELECT_new_id_max_allele_len" type="select" label="Set New id max allele len" help="Specify maximum number of leading characters from allele codes to include in new variant IDs, and behavior on longer codes (defaults 23, error)." argument="--new-id-max-allele-len">
6146 <option value="no_set" selected="True">Don't set</option>
6147 <option value="set">Set value(s)</option>
6148 </param>
6149 <when value="no_set">
6150 </when>
6151 <when value="set">
6152
6153 <param name="new_id_max_allele_len_MOD_0_0" type="text" label="len" value="" optional="True" argument="len" help=""/>
6154 <conditional name="CONDITIONAL_new_id_max_allele_len_MOD_1">
6155 <param name="CONDITIONAL_SELECT_new_id_max_allele_len_MOD_1" type="select" label="How to set New id max allele len">
6156 <option value="no_set" selected="True">Don't set</option>
6157 <option value="from_list">Select from list</option>
6158
6159 </param>
6160 <when value="no_set">
6161 </when>
6162
6163 <when value="from_list">
6164 <param name="new_id_max_allele_len_MOD_1" type="select" label="Select value">
6165 <option value="{error">{error</option>
6166 <option value="missing">missing</option>
6167 <option value="truncate}">truncate}</option>
6168 </param>
6169 </when>
6170 </conditional>
6171 </when>
6172 </conditional>
6173 <conditional name="CONDITIONAL_missing_var_code">
6174 <param name="CONDITIONAL_SELECT_missing_var_code" type="select" label="Set Missing var code" help="Change unnamed variant code for --rm-dup, --set-{missing|all}-var-ids, and --recover-var-ids (default '.'). " argument="--missing-var-code">
6175 <option value="no_set" selected="True">Don't set</option>
6176 <option value="set">Set value(s)</option>
6177 </param>
6178 <when value="no_set">
6179 </when>
6180 <when value="set">
6181
6182 <param name="missing_var_code_MOD_0_0" type="text" label="str" value="" optional="True" argument="str" help=""/>
6183 </when>
6184 </conditional>
6185 <conditional name="CONDITIONAL_update_map">
6186 <param name="CONDITIONAL_SELECT_update_map" type="select" label="Set Update map" help="Update variant bp positions. " argument="--update-map">
6187 <option value="no_set" selected="True">Don't set</option>
6188 <option value="set">Set value(s)</option>
6189 </param>
6190 <when value="no_set">
6191 </when>
6192 <when value="set">
6193
6194 <param name="update_map_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
6195 <param name="update_map_MOD_1_0" type="text" label="bpcol" value="" optional="False" argument="bpcol" help=""/>
6196 <param name="update_map_MOD_2_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/>
6197 <param name="update_map_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
6198 </when>
6199 </conditional>
6200 <conditional name="CONDITIONAL_update_name">
6201 <param name="CONDITIONAL_SELECT_update_name" type="select" label="Set Update name" help="Update variant IDs. " argument="--update-name">
6202 <option value="no_set" selected="True">Don't set</option>
6203 <option value="set">Set value(s)</option>
6204 </param>
6205 <when value="no_set">
6206 </when>
6207 <when value="set">
6208
6209 <param name="update_name_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
6210 <param name="update_name_MOD_1_0" type="text" label="newcol" value="" optional="False" argument="newcol" help=""/>
6211 <param name="update_name_MOD_2_0" type="text" label="oldcol" value="" optional="False" argument="oldcol" help=""/>
6212 <param name="update_name_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
6213 </when>
6214 </conditional>
6215 <conditional name="CONDITIONAL_recover_var_ids">
6216 <param name="CONDITIONAL_SELECT_recover_var_ids" type="select" label="Set Recover var ids" help="Undo --set-all-var-ids, given the original .pvar/VCF/.bim file. Original IDs are looked up by position and allele codes. * By default, if the original-ID file is a .bim, allele order is ignored. Use 'strict-bim-order' to force A1=ALT, A2=REF. * If any variant has multiple matching records in the original-ID file, and the IDs conflict, --recover-var-ids writes the affected (current) ID(s) to &lt;output prefix&gt;.recoverid.dup, and normally errors out. If the original-ID file has the same number of variants in the same order, you can still recover the old IDs with the 'rigid' modifier in this case. Alternatively, to proceed and assign the missing-ID code to these variants, add the 'force' modifier. (The .recoverid.dup file is still written when 'rigid' or 'force' is specified.) * --recover-var-ids normally expects to replace all variant IDs, and errors out if any are left untouched. Add the 'partial' modifier when you actually want to update just a proper subset." argument="--recover-var-ids">
6217 <option value="no_set" selected="True">Don't set</option>
6218 <option value="set">Set value(s)</option>
6219 </param>
6220 <when value="no_set">
6221 </when>
6222 <when value="set">
6223
6224 <param name="recover_var_ids_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/>
6225 <param name="recover_var_ids_MOD_1_0" type="text" label="'strict-bim-order'" value="" optional="False" argument="'strict-bim-order'" help=""/>
6226 <conditional name="CONDITIONAL_recover_var_ids_MOD_2">
6227 <param name="CONDITIONAL_SELECT_recover_var_ids_MOD_2" type="select" label="How to set Recover var ids">
6228 <option value="no_set" selected="True">Don't set</option>
6229 <option value="from_list">Select from list</option>
6230
6231 </param>
6232 <when value="no_set">
6233 </when>
6234
6235 <when value="from_list">
6236 <param name="recover_var_ids_MOD_2" type="select" label="Select value">
6237 <option value="{rigid">{rigid</option>
6238 <option value="force}">force}</option>
6239 </param>
6240 </when>
6241 </conditional>
6242 <param name="recover_var_ids_MOD_3_0" type="text" label="'partial'" value="" optional="False" argument="'partial'" help=""/>
6243 </when>
6244 </conditional>
6245 <conditional name="CONDITIONAL_update_alleles">
6246 <param name="CONDITIONAL_SELECT_update_alleles" type="select" label="Set Update alleles" help="Update variant allele codes. " argument="--update-alleles">
6247 <option value="no_set" selected="True">Don't set</option>
6248 <option value="set">Set value(s)</option>
6249 </param>
6250 <when value="no_set">
6251 </when>
6252 <when value="set">
6253
6254 <param name="update_alleles_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/>
6255 </when>
6256 </conditional>
6257 <conditional name="CONDITIONAL_update_ids">
6258 <param name="CONDITIONAL_SELECT_update_ids" type="select" label="Set Update ids" help="Update sample IDs. " argument="--update-ids">
6259 <option value="no_set" selected="True">Don't set</option>
6260 <option value="set">Set value(s)</option>
6261 </param>
6262 <when value="no_set">
6263 </when>
6264 <when value="set">
6265
6266 <param name="update_ids_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/>
6267 </when>
6268 </conditional>
6269 <conditional name="CONDITIONAL_update_parents">
6270 <param name="CONDITIONAL_SELECT_update_parents" type="select" label="Set Update parents" help="Update parental IDs. " argument="--update-parents">
6271 <option value="no_set" selected="True">Don't set</option>
6272 <option value="set">Set value(s)</option>
6273 </param>
6274 <when value="no_set">
6275 </when>
6276 <when value="set">
6277
6278 <param name="update_parents_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/>
6279 </when>
6280 </conditional>
6281 <conditional name="CONDITIONAL_update_sex">
6282 <param name="CONDITIONAL_SELECT_update_sex" type="select" label="Set Update sex" help="Update sex information. * By default, if there is a header line starting with '#FID'/'#IID', sex is loaded from the first column titled 'SEX' (any capitalization); otherwise, column 3 is assumed. Use 'col-num=' to force a column number. * Only the first character in the sex column is processed. By default, '1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female, and '0'/'N' is interpreted as unknown-sex. To change this to '0'/'M'/'m' = male, '1'/'F'/'f' = female, anything else other than '2' = unknown-sex, add 'male0'." argument="--update-sex">
6283 <option value="no_set" selected="True">Don't set</option>
6284 <option value="set">Set value(s)</option>
6285 </param>
6286 <when value="no_set">
6287 </when>
6288 <when value="set">
6289
6290 <param name="update_sex_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
6291 <param name="update_sex_MOD_1_0" type="text" label="'col-num='&lt;n&gt;" value="" optional="False" argument="'col-num='&lt;n&gt;" help=""/>
6292 <param name="update_sex_MOD_2_0" type="text" label="'male0'" value="" optional="False" argument="'male0'" help=""/>
6293 </when>
6294 </conditional>
6295 <conditional name="CONDITIONAL_real_ref_alleles">
6296 <param name="CONDITIONAL_SELECT_real_ref_alleles" type="select" label="Set Real ref alleles" help="Treat A2 alleles in a PLINK 1.x fileset as actual REF alleles; otherwise they're marked as provisional. " argument="--real-ref-alleles">
6297 <option value="no_set" selected="True">Don't set</option>
6298 <option value="set">Set value(s)</option>
6299 </param>
6300 <when value="no_set">
6301 </when>
6302 <when value="set">
6303
6304 </when>
6305 </conditional>
6306 <conditional name="CONDITIONAL_maj_ref">
6307 <param name="CONDITIONAL_SELECT_maj_ref" type="select" label="Set Maj ref" help="Set major alleles to reference, like PLINK 1.x automatically did. (Note that this is now opt-in rather than opt-out; --keep-allele-order is no longer necessary to prevent allele-swapping.) * This can only be used in runs with --make-bed/--make-[b]pgen/--export and no other commands. * By default, this only affects variants marked as having 'provisional' reference alleles. Add 'force' to apply this to all variants. * All new reference alleles are marked as provisional. " argument="--maj-ref">
6308 <option value="no_set" selected="True">Don't set</option>
6309 <option value="set">Set value(s)</option>
6310 </param>
6311 <when value="no_set">
6312 </when>
6313 <when value="set">
6314
6315 <param name="maj_ref_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/>
6316 </when>
6317 </conditional>
6318 <conditional name="CONDITIONAL_ref_allele">
6319 <param name="CONDITIONAL_SELECT_ref_allele" type="select" label="Set Ref allele" help="" argument="--ref-allele">
6320 <option value="no_set" selected="True">Don't set</option>
6321 <option value="set">Set value(s)</option>
6322 </param>
6323 <when value="no_set">
6324 </when>
6325 <when value="set">
6326
6327 <param name="ref_allele_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/>
6328 <param name="ref_allele_MOD_1_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
6329 <param name="ref_allele_MOD_2_0" type="text" label="refcol" value="" optional="False" argument="refcol" help=""/>
6330 <param name="ref_allele_MOD_3_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/>
6331 <param name="ref_allele_MOD_4_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
6332 </when>
6333 </conditional>
6334 <conditional name="CONDITIONAL_alt1_allele">
6335 <param name="CONDITIONAL_SELECT_alt1_allele" type="select" label="Set Alt1 allele" help="These set the alleles specified in the file to ref (--ref-allele) or alt1 (--alt1-allele). They can be combined in the same run. * These can only be used in runs with --make-bed/--make-[b]pgen/--export and no other commands. * &quot;--ref-allele &lt;VCF filename&gt; 4 3 '#'&quot;, which scrapes reference allele assignments from a VCF file, is especially useful. * By default, these error out when asked to change a 'known' reference allele. Add 'force' to permit that (when e.g. switching to a new reference genome). * When --alt1-allele changes the previous ref allele to alt1, the previous alt1 allele is set to reference and marked as provisional." argument="--alt1-allele">
6336 <option value="no_set" selected="True">Don't set</option>
6337 <option value="set">Set value(s)</option>
6338 </param>
6339 <when value="no_set">
6340 </when>
6341 <when value="set">
6342
6343 <param name="alt1_allele_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/>
6344 <param name="alt1_allele_MOD_1_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
6345 <param name="alt1_allele_MOD_2_0" type="text" label="alt1col" value="" optional="False" argument="alt1col" help=""/>
6346 <param name="alt1_allele_MOD_3_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/>
6347 <param name="alt1_allele_MOD_4_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
6348 </when>
6349 </conditional>
6350 <conditional name="CONDITIONAL_ref_from_fa">
6351 <param name="CONDITIONAL_SELECT_ref_from_fa" type="select" label="Set Ref from fa" help="This sets reference alleles from the --fa file when it can be done unambiguously (note that it's never possible for deletions or some insertions). By default, it errors out when asked to change a 'known' reference allele; add the 'force' modifier to permit that. " argument="--ref-from-fa">
6352 <option value="no_set" selected="True">Don't set</option>
6353 <option value="set">Set value(s)</option>
6354 </param>
6355 <when value="no_set">
6356 </when>
6357 <when value="set">
6358
6359 <param name="ref_from_fa_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/>
6360 </when>
6361 </conditional>
6362 <conditional name="CONDITIONAL_normalize">
6363 <param name="CONDITIONAL_SELECT_normalize" type="select" label="Set Normalize" help="Left-normalize all variants, using the --fa file. (alias: --norm) (Assumes no differences in capitalization.) The 'list' modifier causes a list of affected variant IDs to be written to &lt;output prefix&gt;.normalized." argument="--normalize">
6364 <option value="no_set" selected="True">Don't set</option>
6365 <option value="set">Set value(s)</option>
6366 </param>
6367 <when value="no_set">
6368 </when>
6369 <when value="set">
6370
6371 <param name="normalize_MOD_0_0" type="text" label="'list'" value="" optional="False" argument="'list'" help=""/>
6372 </when>
6373 </conditional>
6374 <conditional name="CONDITIONAL_indiv_sort">
6375 <param name="CONDITIONAL_SELECT_indiv_sort" type="select" label="Set Indiv sort" help="Specify sample ID sort order for merge and --make-[b]pgen/--make-bed. The following four modes are supported: * 'none'/'0' keeps samples in the order they were loaded. Default for non-merge. * 'natural'/'n' invokes &quot;natural sort&quot;, e.g. 'id2' &lt; 'ID3' &lt; 'id10'. Default when merging. * 'ascii'/'a' sorts in ASCII order, e.g. 'ID3' &lt; 'id10' &lt; 'id2'. * 'file'/'f' uses the order in the given file (named in the last parameter). " argument="--indiv-sort">
6376 <option value="no_set" selected="True">Don't set</option>
6377 <option value="set">Set value(s)</option>
6378 </param>
6379 <when value="no_set">
6380 </when>
6381 <when value="set">
6382
6383 <param name="indiv_sort_MOD_0_0" type="text" label="mode" value="" optional="True" argument="mode" help=""/>
6384 <param name="indiv_sort_MOD_1_0" type="data" format="txt" label="f" multiple="False" optional="False" argument="f"/>
6385 </when>
6386 </conditional>
6387 <conditional name="CONDITIONAL_king_table_filter">
6388 <param name="CONDITIONAL_SELECT_king_table_filter" type="select" label="Set King table filter" help="Specify minimum kinship coefficient for inclusion in --make-king-table report. " argument="--king-table-filter">
6389 <option value="no_set" selected="True">Don't set</option>
6390 <option value="set">Set value(s)</option>
6391 </param>
6392 <when value="no_set">
6393 </when>
6394 <when value="set">
6395
6396 <param name="king_table_filter_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/>
6397 </when>
6398 </conditional>
6399 <conditional name="CONDITIONAL_king_table_subset">
6400 <param name="CONDITIONAL_SELECT_king_table_subset" type="select" label="Set King table subset" help="Restrict current --make-king-table run to sample pairs listed in the given .kin0 file. If a second parameter is provided, only sample pairs with kinship &gt;= that threshold (in the input .kin0) are processed. " argument="--king-table-subset">
6401 <option value="no_set" selected="True">Don't set</option>
6402 <option value="set">Set value(s)</option>
6403 </param>
6404 <when value="no_set">
6405 </when>
6406 <when value="set">
6407
6408 <param name="king_table_subset_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
6409 <param name="king_table_subset_MOD_1_0" type="text" label="kmin" value="" optional="False" argument="kmin" help=""/>
6410 </when>
6411 </conditional>
6412 <conditional name="CONDITIONAL_condition">
6413 <param name="CONDITIONAL_SELECT_condition" type="select" label="Set Condition" help="" argument="--condition">
6414 <option value="no_set" selected="True">Don't set</option>
6415 <option value="set">Set value(s)</option>
6416 </param>
6417 <when value="no_set">
6418 </when>
6419 <when value="set">
6420
6421 <param name="condition_MOD_0_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/>
6422 <conditional name="CONDITIONAL_condition_MOD_1">
6423 <param name="CONDITIONAL_SELECT_condition_MOD_1" type="select" label="How to set Condition">
6424 <option value="no_set" selected="True">Don't set</option>
6425 <option value="from_list">Select from list</option>
6426
6427 </param>
6428 <when value="no_set">
6429 </when>
6430
6431 <when value="from_list">
6432 <param name="condition_MOD_1" type="select" label="Select value">
6433 <option value="{dominant">{dominant</option>
6434 <option value="recessive}">recessive}</option>
6435 </param>
6436 </when>
6437 </conditional>
6438 <param name="condition_MOD_2_0" type="text" label="'multiallelic'" value="" optional="False" argument="'multiallelic'" help=""/>
6439 </when>
6440 </conditional>
6441 <conditional name="CONDITIONAL_condition_list">
6442 <param name="CONDITIONAL_SELECT_condition_list" type="select" label="Set Condition list" help="Add the given variant, or all variants in the given file, as --glm covariates. By default, this errors out if any of the variants are multiallelic; add the 'multiallelic' ('m' for short) modifier to allow them. They'll effectively be split against the major allele (unless --glm's 'omit-ref' modifier was specified), and all induced covariate names--even for biallelic variants--will have an underscore followed by the allele code at the end." argument="--condition-list">
6443 <option value="no_set" selected="True">Don't set</option>
6444 <option value="set">Set value(s)</option>
6445 </param>
6446 <when value="no_set">
6447 </when>
6448 <when value="set">
6449
6450 <param name="condition_list_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/>
6451 <conditional name="CONDITIONAL_condition_list_MOD_1">
6452 <param name="CONDITIONAL_SELECT_condition_list_MOD_1" type="select" label="How to set Condition list">
6453 <option value="no_set" selected="True">Don't set</option>
6454 <option value="from_list">Select from list</option>
6455
6456 </param>
6457 <when value="no_set">
6458 </when>
6459
6460 <when value="from_list">
6461 <param name="condition_list_MOD_1" type="select" label="Select value">
6462 <option value="{dominant">{dominant</option>
6463 <option value="recessive}">recessive}</option>
6464 </param>
6465 </when>
6466 </conditional>
6467 <param name="condition_list_MOD_2_0" type="text" label="'multiallelic'" value="" optional="False" argument="'multiallelic'" help=""/>
6468 </when>
6469 </conditional>
6470 <conditional name="CONDITIONAL_parameters">
6471 <param name="CONDITIONAL_SELECT_parameters" type="select" label="Set Parameters" help="Include only the given covariates/interactions in the --glm model, identified by a list of 1-based indices and/or ranges of them. " argument="--parameters">
6472 <option value="no_set" selected="True">Don't set</option>
6473 <option value="set">Set value(s)</option>
6474 </param>
6475 <when value="no_set">
6476 </when>
6477 <when value="set">
6478
6479 <param name="parameters_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
6480 </when>
6481 </conditional>
6482 <conditional name="CONDITIONAL_OVERLOADED_tests">
6483 <param name="CONDITIONAL_OVERLOADED_SELECT_tests" type="select" label="Choose argument form for Tests" help="Overloaded argument, must chose a form">
6484 <option value="form_0">Form 0</option>
6485 <option value="form_1">Form 1</option>
6486 </param>
6487 <when value="form_0">
6488
6489 <conditional name="CONDITIONAL_tests">
6490 <param name="CONDITIONAL_SELECT_tests" type="select" label="Set Tests" help="Perform a (joint) test on the specified term(s) in the " argument="--tests">
6491 <option value="no_set" selected="True">Don't set</option>
6492 <option value="set">Set value(s)</option>
6493 </param>
6494 <when value="no_set">
6495 </when>
6496 <when value="set">
6497
6498 <param name="tests_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
6499 </when>
6500 </conditional>
6501 </when>
6502 <when value="form_1">
6503
6504 <conditional name="CONDITIONAL_tests">
6505 <param name="CONDITIONAL_SELECT_tests" type="select" label="Set Tests" help="" argument="--tests">
6506 <option value="no_set" selected="True">Don't set</option>
6507 <option value="set">Set value(s)</option>
6508 </param>
6509 <when value="no_set">
6510 </when>
6511 <when value="set">
6512
6513 </when>
6514 </conditional>
6515 </when>
6516 </conditional>
6517 <conditional name="CONDITIONAL_vif">
6518 <param name="CONDITIONAL_SELECT_vif" type="select" label="Set Vif" help="Set VIF threshold for --glm multicollinearity check (default 50). (This is no longer skipped for case/control phenotypes.) " argument="--vif">
6519 <option value="no_set" selected="True">Don't set</option>
6520 <option value="set">Set value(s)</option>
6521 </param>
6522 <when value="no_set">
6523 </when>
6524 <when value="set">
6525
6526 <param name="vif_MOD_0_0" type="text" label="max VIF" value="" optional="True" argument="max VIF" help=""/>
6527 </when>
6528 </conditional>
6529 <conditional name="CONDITIONAL_max_corr">
6530 <param name="CONDITIONAL_SELECT_max_corr" type="select" label="Set Max corr" help="Skip --glm regression when the absolute value of the correlation between two predictors exceeds this value (default 0.999). " argument="--max-corr">
6531 <option value="no_set" selected="True">Don't set</option>
6532 <option value="set">Set value(s)</option>
6533 </param>
6534 <when value="no_set">
6535 </when>
6536 <when value="set">
6537
6538 <param name="max_corr_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
6539 </when>
6540 </conditional>
6541 <conditional name="CONDITIONAL_xchr_model">
6542 <param name="CONDITIONAL_SELECT_xchr_model" type="select" label="Set Xchr model" help="Set the chrX --glm/--condition[-list]/--[v]score model. * '0' = skip chrX. * '1' = add sex as a covar on chrX, code males 0..1. * '2' (default) = chrX sex covar, code males 0..2. (Use the --glm 'interaction' modifier to test for interaction between genotype and sex.) " argument="--xchr-model">
6543 <option value="no_set" selected="True">Don't set</option>
6544 <option value="set">Set value(s)</option>
6545 </param>
6546 <when value="no_set">
6547 </when>
6548 <when value="set">
6549
6550 <param name="xchr_model_MOD_0_0" type="text" label="m" value="" optional="True" argument="m" help=""/>
6551 </when>
6552 </conditional>
6553 <conditional name="CONDITIONAL_adjust">
6554 <param name="CONDITIONAL_SELECT_adjust" type="select" label="Set Adjust" help="For each association test in this run, report some basic multiple-testing corrections, sorted in increasing-p-value order. Modifiers work the same way as they do on --adjust-file." argument="--adjust">
6555 <option value="no_set" selected="True">Don't set</option>
6556 <option value="set">Set value(s)</option>
6557 </param>
6558 <when value="no_set">
6559 </when>
6560 <when value="set">
6561
6562 <param name="adjust_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
6563 <param name="adjust_MOD_1_0" type="text" label="'gc'" value="" optional="False" argument="'gc'" help=""/>
6564 <param name="adjust_MOD_2_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/>
6565 <param name="adjust_MOD_3_0" type="text" label="'cols='&lt;column set descriptor&gt;" value="" optional="False" argument="'cols='&lt;column set descriptor&gt;" help=""/>
6566 </when>
6567 </conditional>
6568 <conditional name="CONDITIONAL_lambda">
6569 <param name="CONDITIONAL_SELECT_lambda" type="select" label="Set Lambda" help="Set genomic control lambda for --adjust[-file]. " argument="--lambda">
6570 <option value="no_set" selected="True">Don't set</option>
6571 <option value="set">Set value(s)</option>
6572 </param>
6573 <when value="no_set">
6574 </when>
6575 <when value="set">
6576
6577 </when>
6578 </conditional>
6579 <conditional name="CONDITIONAL_adjust_chr_field">
6580 <param name="CONDITIONAL_SELECT_adjust_chr_field" type="select" label="Set Adjust chr field" help="Set --adjust-file input field names. When " argument="--adjust-chr-field">
6581 <option value="no_set" selected="True">Don't set</option>
6582 <option value="set">Set value(s)</option>
6583 </param>
6584 <when value="no_set">
6585 </when>
6586 <when value="set">
6587
6588 <param name="adjust_chr_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
6589 </when>
6590 </conditional>
6591 <conditional name="CONDITIONAL_adjust_pos_field">
6592 <param name="CONDITIONAL_SELECT_adjust_pos_field" type="select" label="Set Adjust pos field" help="" argument="--adjust-pos-field">
6593 <option value="no_set" selected="True">Don't set</option>
6594 <option value="set">Set value(s)</option>
6595 </param>
6596 <when value="no_set">
6597 </when>
6598 <when value="set">
6599
6600 <param name="adjust_pos_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
6601 </when>
6602 </conditional>
6603 <conditional name="CONDITIONAL_adjust_id_field">
6604 <param name="CONDITIONAL_SELECT_adjust_id_field" type="select" label="Set Adjust id field" help="" argument="--adjust-id-field">
6605 <option value="no_set" selected="True">Don't set</option>
6606 <option value="set">Set value(s)</option>
6607 </param>
6608 <when value="no_set">
6609 </when>
6610 <when value="set">
6611
6612 <param name="adjust_id_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
6613 </when>
6614 </conditional>
6615 <conditional name="CONDITIONAL_adjust_ref_field">
6616 <param name="CONDITIONAL_SELECT_adjust_ref_field" type="select" label="Set Adjust ref field" help="" argument="--adjust-ref-field">
6617 <option value="no_set" selected="True">Don't set</option>
6618 <option value="set">Set value(s)</option>
6619 </param>
6620 <when value="no_set">
6621 </when>
6622 <when value="set">
6623
6624 <param name="adjust_ref_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
6625 </when>
6626 </conditional>
6627 <conditional name="CONDITIONAL_adjust_alt_field">
6628 <param name="CONDITIONAL_SELECT_adjust_alt_field" type="select" label="Set Adjust alt field" help="" argument="--adjust-alt-field">
6629 <option value="no_set" selected="True">Don't set</option>
6630 <option value="set">Set value(s)</option>
6631 </param>
6632 <when value="no_set">
6633 </when>
6634 <when value="set">
6635
6636 <param name="adjust_alt_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
6637 </when>
6638 </conditional>
6639 <conditional name="CONDITIONAL_adjust_a1_field">
6640 <param name="CONDITIONAL_SELECT_adjust_a1_field" type="select" label="Set Adjust a1 field" help="" argument="--adjust-a1-field">
6641 <option value="no_set" selected="True">Don't set</option>
6642 <option value="set">Set value(s)</option>
6643 </param>
6644 <when value="no_set">
6645 </when>
6646 <when value="set">
6647
6648 <param name="adjust_a1_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
6649 </when>
6650 </conditional>
6651 <conditional name="CONDITIONAL_adjust_test_field">
6652 <param name="CONDITIONAL_SELECT_adjust_test_field" type="select" label="Set Adjust test field" help="" argument="--adjust-test-field">
6653 <option value="no_set" selected="True">Don't set</option>
6654 <option value="set">Set value(s)</option>
6655 </param>
6656 <when value="no_set">
6657 </when>
6658 <when value="set">
6659
6660 <param name="adjust_test_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
6661 </when>
6662 </conditional>
6663 <conditional name="CONDITIONAL_adjust_p_field">
6664 <param name="CONDITIONAL_SELECT_adjust_p_field" type="select" label="Set Adjust p field" help="" argument="--adjust-p-field">
6665 <option value="no_set" selected="True">Don't set</option>
6666 <option value="set">Set value(s)</option>
6667 </param>
6668 <when value="no_set">
6669 </when>
6670 <when value="set">
6671
6672 <param name="adjust_p_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
6673 </when>
6674 </conditional>
6675 <conditional name="CONDITIONAL_ci">
6676 <param name="CONDITIONAL_SELECT_ci" type="select" label="Set Ci" help="Report confidence ratios for odds ratios/betas. " argument="--ci">
6677 <option value="no_set" selected="True">Don't set</option>
6678 <option value="set">Set value(s)</option>
6679 </param>
6680 <when value="no_set">
6681 </when>
6682 <when value="set">
6683
6684 <param name="ci_MOD_0_0" type="text" label="size" value="" optional="True" argument="size" help=""/>
6685 </when>
6686 </conditional>
6687 <conditional name="CONDITIONAL_pfilter">
6688 <param name="CONDITIONAL_SELECT_pfilter" type="select" label="Set Pfilter" help="Filter out assoc. test results with higher p-values. " argument="--pfilter">
6689 <option value="no_set" selected="True">Don't set</option>
6690 <option value="set">Set value(s)</option>
6691 </param>
6692 <when value="no_set">
6693 </when>
6694 <when value="set">
6695
6696 <param name="pfilter_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
6697 </when>
6698 </conditional>
6699 <conditional name="CONDITIONAL_score_col_nums">
6700 <param name="CONDITIONAL_SELECT_score_col_nums" type="select" label="Set Score col nums" help="Process all the specified coefficient columns in the --score file, identified by 1-based indexes and/or ranges of them. " argument="--score-col-nums">
6701 <option value="no_set" selected="True">Don't set</option>
6702 <option value="set">Set value(s)</option>
6703 </param>
6704 <when value="no_set">
6705 </when>
6706 <when value="set">
6707
6708 <param name="score_col_nums_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
6709 </when>
6710 </conditional>
6711 <conditional name="CONDITIONAL_q_score_range">
6712 <param name="CONDITIONAL_SELECT_q_score_range" type="select" label="Set Q score range" help="Apply --score to subset(s) of variants in the primary score list(s) based on e.g. p-value ranges. * The first file should have range labels in the first column, p-value lower bounds in the second column, and upper bounds in the third column. Lines with too few entries, or nonnumeric values in the second or third column, are ignored. * The second file should contain a variant ID and a p-value on each line (except possibly the first). Variant IDs are read from column #i and p-values are read from column #j, where i defaults to 1 and j defaults to i+1. The 'header' modifier causes the first nonempty line of this file to be skipped. * By default, --q-score-range errors out when a variant ID appears multiple times in the data file (and is also present in the main dataset). To use the minimum p-value in this case instead, add the 'min' modifier." argument="--q-score-range">
6713 <option value="no_set" selected="True">Don't set</option>
6714 <option value="set">Set value(s)</option>
6715 </param>
6716 <when value="no_set">
6717 </when>
6718 <when value="set">
6719
6720 <param name="q_score_range_MOD_0_0" type="text" label="range file" value="" optional="True" argument="range file" help=""/>
6721 <param name="q_score_range_MOD_1_0" type="text" label="data file" value="" optional="True" argument="data file" help=""/>
6722 <param name="q_score_range_MOD_2_0" type="text" label="i" value="" optional="False" argument="i" help=""/>
6723 <param name="q_score_range_MOD_3_0" type="text" label="j" value="" optional="False" argument="j" help=""/>
6724 <param name="q_score_range_MOD_4_0" type="text" label="'header'" value="" optional="False" argument="'header'" help=""/>
6725 <param name="q_score_range_MOD_5_0" type="text" label="'min'" value="" optional="False" argument="'min'" help=""/>
6726 </when>
6727 </conditional>
6728 <conditional name="CONDITIONAL_vscore_col_nums">
6729 <param name="CONDITIONAL_SELECT_vscore_col_nums" type="select" label="Set Vscore col nums" help="Process all the specified coefficient columns in the --variant-score file, identified by 1-based indexes and/or ranges of them. " argument="--vscore-col-nums">
6730 <option value="no_set" selected="True">Don't set</option>
6731 <option value="set">Set value(s)</option>
6732 </param>
6733 <when value="no_set">
6734 </when>
6735 <when value="set">
6736
6737 <param name="vscore_col_nums_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
6738 </when>
6739 </conditional>
6740 <conditional name="CONDITIONAL_memory">
6741 <param name="CONDITIONAL_SELECT_memory" type="select" label="Set Memory" help="Set size, in MiB, of initial workspace malloc attempt. To error out instead of reducing the request size when the initial attempt fails, add the 'require' modifier. " argument="--memory">
6742 <option value="no_set" selected="True">Don't set</option>
6743 <option value="set">Set value(s)</option>
6744 </param>
6745 <when value="no_set">
6746 </when>
6747 <when value="set">
6748
6749 <param name="memory_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
6750 <param name="memory_MOD_1_0" type="text" label="'require'" value="" optional="False" argument="'require'" help=""/>
6751 </when>
6752 </conditional>
6753 <conditional name="CONDITIONAL_threads">
6754 <param name="CONDITIONAL_SELECT_threads" type="select" label="Set Threads" help="Set maximum number of compute threads. " argument="--threads">
6755 <option value="no_set" selected="True">Don't set</option>
6756 <option value="set">Set value(s)</option>
6757 </param>
6758 <when value="no_set">
6759 </when>
6760 <when value="set">
6761
6762 <param name="threads_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
6763 </when>
6764 </conditional>
6765 <conditional name="CONDITIONAL_d">
6766 <param name="CONDITIONAL_SELECT_d" type="select" label="Set D" help="Change variant/covariate range delimiter (normally '-'). " argument="--d">
6767 <option value="no_set" selected="True">Don't set</option>
6768 <option value="set">Set value(s)</option>
6769 </param>
6770 <when value="no_set">
6771 </when>
6772 <when value="set">
6773
6774 <param name="d_MOD_0_0" type="text" label="char" value="" optional="True" argument="char" help=""/>
6775 </when>
6776 </conditional>
6777 <conditional name="CONDITIONAL_seed">
6778 <param name="CONDITIONAL_SELECT_seed" type="select" label="Set Seed" help='Set random number seed(s). Each value must be an integer between 0 and 4294967295 inclusive. Note that --threads and "--memory require" may also be needed to reproduce some randomized runs. ' argument="--seed">
6779 <option value="no_set" selected="True">Don't set</option>
6780 <option value="set">Set value(s)</option>
6781 </param>
6782 <when value="no_set">
6783 </when>
6784 <when value="set">
6785
6786 <param name="seed_MOD_0_0" type="text" label="val..." value="" optional="True" argument="val..." help="Multiple values are allowed"/>
6787 </when>
6788 </conditional>
6789 <conditional name="CONDITIONAL_output_min_p">
6790 <param name="CONDITIONAL_SELECT_output_min_p" type="select" label="Set Output min p" help="Specify minimum p-value to write to reports. (2.23e-308 is useful for preventing underflow in some programs.) " argument="--output-min-p">
6791 <option value="no_set" selected="True">Don't set</option>
6792 <option value="set">Set value(s)</option>
6793 </param>
6794 <when value="no_set">
6795 </when>
6796 <when value="set">
6797
6798 <param name="output_min_p_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/>
6799 </when>
6800 </conditional>
6801 <conditional name="CONDITIONAL_debug">
6802 <param name="CONDITIONAL_SELECT_debug" type="select" label="Set Debug" help="Use slower, more crash-resistant logging method. " argument="--debug">
6803 <option value="no_set" selected="True">Don't set</option>
6804 <option value="set">Set value(s)</option>
6805 </param>
6806 <when value="no_set">
6807 </when>
6808 <when value="set">
6809
6810 </when>
6811 </conditional>
6812 <conditional name="CONDITIONAL_randmem">
6813 <param name="CONDITIONAL_SELECT_randmem" type="select" label="Set Randmem" help="Randomize initial workspace memory (helps catch uninitialized-memory bugs). " argument="--randmem">
6814 <option value="no_set" selected="True">Don't set</option>
6815 <option value="set">Set value(s)</option>
6816 </param>
6817 <when value="no_set">
6818 </when>
6819 <when value="set">
6820
6821 </when>
6822 </conditional>
6823 <conditional name="CONDITIONAL_warning_errcode">
6824 <param name="CONDITIONAL_SELECT_warning_errcode" type="select" label="Set Warning errcode" help="Return a nonzero error code to the OS when a run completes with warning(s). " argument="--warning-errcode">
6825 <option value="no_set" selected="True">Don't set</option>
6826 <option value="set">Set value(s)</option>
6827 </param>
6828 <when value="no_set">
6829 </when>
6830 <when value="set">
6831
6832 </when>
6833 </conditional>
6834 <conditional name="CONDITIONAL_zst_level">
6835 <param name="CONDITIONAL_SELECT_zst_level" type="select" label="Set Zst level" help="Set the Zstd compression level (1-22, default 3). " argument="--zst-level">
6836 <option value="no_set" selected="True">Don't set</option>
6837 <option value="set">Set value(s)</option>
6838 </param>
6839 <when value="no_set">
6840 </when>
6841 <when value="set">
6842
6843 <param name="zst_level_MOD_0_0" type="text" label="lvl" value="" optional="True" argument="lvl" help=""/>
6844 </when>
6845 </conditional>
6846 </inputs>
6847 <outputs>
6848 <data name="OUTPUT_plink_acount __freq" format="plink.acount --freq" label="${tool.name} on ${on_string}: plink.acount --freq" from_work_dir="plink.acount --freq" hidden="True"/>
6849 <data name="OUTPUT_plink_adjusted __adjust_" format="plink.adjusted --adjust," label="${tool.name} on ${on_string}: plink.adjusted --adjust," from_work_dir="plink.adjusted --adjust," hidden="True"/>
6850 <data name="OUTPUT_plink_afreq __freq Allele" format="plink.afreq --freq Allele" label="${tool.name} on ${on_string}: plink.afreq --freq Allele" from_work_dir="plink.afreq --freq Allele" hidden="True"/>
6851 <data name="OUTPUT_plink_bcf __export" format="plink.bcf --export" label="${tool.name} on ${on_string}: plink.bcf --export" from_work_dir="plink.bcf --export" hidden="True"/>
6852 <data name="OUTPUT_plink_bed __make_bed___ PLINK" format="plink.bed --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.bed --make-bed... PLINK" from_work_dir="plink.bed --make-bed... PLINK" hidden="True"/>
6853 <data name="OUTPUT_plink_bgen __export" format="plink.bgen --export" label="${tool.name} on ${on_string}: plink.bgen --export" from_work_dir="plink.bgen --export" hidden="True"/>
6854 <data name="OUTPUT_plink_bim __make_bed___ PLINK" format="plink.bim --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.bim --make-bed... PLINK" from_work_dir="plink.bim --make-bed... PLINK" hidden="True"/>
6855 <data name="OUTPUT_plink_bin several Matrix" format="plink.bin several Matrix" label="${tool.name} on ${on_string}: plink.bin several Matrix" from_work_dir="plink.bin several Matrix" hidden="True"/>
6856 <data name="OUTPUT_plink_bins __freq" format="plink.bins --freq" label="${tool.name} on ${on_string}: plink.bins --freq" from_work_dir="plink.bins --freq" hidden="True"/>
6857 <data name="OUTPUT_plink_cov __write_covar___ Covariate" format="plink.cov --write-covar... Covariate" label="${tool.name} on ${on_string}: plink.cov --write-covar... Covariate" from_work_dir="plink.cov --write-covar... Covariate" hidden="True"/>
6858 <data name="OUTPUT_plink_eigenval __pca Principal" format="plink.eigenval --pca Principal" label="${tool.name} on ${on_string}: plink.eigenval --pca Principal" from_work_dir="plink.eigenval --pca Principal" hidden="True"/>
6859 <collection name="OUTPUT_plink_eigenvec_ __pca Principal" type="list" label="plink.eigenvec*&#9;--pca&#9;Principal" hidden="True">
6860 <discover_datasets pattern="plink\.eigenvec(?P&lt;name&gt;)\&#9;\-\-pca\&#9;Principal" format="plink.eigenvec* --pca Principal"/>
6861 </collection>
6862 <data name="OUTPUT_plink_fam __make_bed___ PLINK" format="plink.fam --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.fam --make-bed... PLINK" from_work_dir="plink.fam --make-bed... PLINK" hidden="True"/>
6863 <data name="OUTPUT_plink_fst_summary __fst Between_population" format="plink.fst.summary --fst Between-population" label="${tool.name} on ${on_string}: plink.fst.summary --fst Between-population" from_work_dir="plink.fst.summary --fst Between-population" hidden="True"/>
6864 <data name="OUTPUT_plink_fst_var __fst Per_variant" format="plink.fst.var --fst Per-variant" label="${tool.name} on ${on_string}: plink.fst.var --fst Per-variant" from_work_dir="plink.fst.var --fst Per-variant" hidden="True"/>
6865 <data name="OUTPUT_plink_gcount __geno_counts Genotype" format="plink.gcount --geno-counts Genotype" label="${tool.name} on ${on_string}: plink.gcount --geno-counts Genotype" from_work_dir="plink.gcount --geno-counts Genotype" hidden="True"/>
6866 <data name="OUTPUT_plink_gen __export" format="plink.gen --export" label="${tool.name} on ${on_string}: plink.gen --export" from_work_dir="plink.gen --export" hidden="True"/>
6867 <data name="OUTPUT_plink_glm_firth __glm" format="plink.glm.firth --glm" label="${tool.name} on ${on_string}: plink.glm.firth --glm" from_work_dir="plink.glm.firth --glm" hidden="True"/>
6868 <data name="OUTPUT_plink_glm_logistic __glm" format="plink.glm.logistic --glm" label="${tool.name} on ${on_string}: plink.glm.logistic --glm" from_work_dir="plink.glm.logistic --glm" hidden="True"/>
6869 <data name="OUTPUT_plink_glm_logistic_hybrid __glm Logistic/Firth" format="plink.glm.logistic.hybrid --glm Logistic/Firth" label="${tool.name} on ${on_string}: plink.glm.logistic.hybrid --glm Logistic/Firth" from_work_dir="plink.glm.logistic.hybrid --glm Logistic/Firth" hidden="True"/>
6870 <data name="OUTPUT_plink_grm __make_grm_list GCTA" format="plink.grm --make-grm-list GCTA" label="${tool.name} on ${on_string}: plink.grm --make-grm-list GCTA" from_work_dir="plink.grm --make-grm-list GCTA" hidden="True"/>
6871 <data name="OUTPUT_plink_grm_N_bin __make_grm_bin GCTA" format="plink.grm.N.bin --make-grm-bin GCTA" label="${tool.name} on ${on_string}: plink.grm.N.bin --make-grm-bin GCTA" from_work_dir="plink.grm.N.bin --make-grm-bin GCTA" hidden="True"/>
6872 <data name="OUTPUT_plink_grm_bin __make_grm_bin GCTA" format="plink.grm.bin --make-grm-bin GCTA" label="${tool.name} on ${on_string}: plink.grm.bin --make-grm-bin GCTA" from_work_dir="plink.grm.bin --make-grm-bin GCTA" hidden="True"/>
6873 <collection name="OUTPUT_plink___gz few BGZipped" type="list" label="plink.*.gz&#9;few&#9;BGZipped" hidden="True">
6874 <discover_datasets pattern="plink\.(?P&lt;name&gt;)\.gz\&#9;few\&#9;BGZipped" format="plink.*.gz few BGZipped"/>
6875 </collection>
6876 <data name="OUTPUT_plink_haps __export" format="plink.haps --export" label="${tool.name} on ${on_string}: plink.haps --export" from_work_dir="plink.haps --export" hidden="True"/>
6877 <data name="OUTPUT_plink_hardy __hardy Hardy_Weinberg" format="plink.hardy --hardy Hardy-Weinberg" label="${tool.name} on ${on_string}: plink.hardy --hardy Hardy-Weinberg" from_work_dir="plink.hardy --hardy Hardy-Weinberg" hidden="True"/>
6878 <data name="OUTPUT_plink_hardy_x __hardy Graffelman_Weir" format="plink.hardy.x --hardy Graffelman-Weir" label="${tool.name} on ${on_string}: plink.hardy.x --hardy Graffelman-Weir" from_work_dir="plink.hardy.x --hardy Graffelman-Weir" hidden="True"/>
6879 <data name="OUTPUT_plink_het __het Inbreeding" format="plink.het --het Inbreeding" label="${tool.name} on ${on_string}: plink.het --het Inbreeding" from_work_dir="plink.het --het Inbreeding" hidden="True"/>
6880 <collection name="OUTPUT_plink___id lots Ordered" type="list" label="plink.*.id&#9;lots&#9;Ordered" hidden="True">
6881 <discover_datasets pattern="plink\.(?P&lt;name&gt;)\.id\&#9;lots\&#9;Ordered" format="plink.*.id lots Ordered"/>
6882 </collection>
6883 <data name="OUTPUT_plink_kin0 __make_king_table KING_robust" format="plink.kin0 --make-king-table KING-robust" label="${tool.name} on ${on_string}: plink.kin0 --make-king-table KING-robust" from_work_dir="plink.kin0 --make-king-table KING-robust" hidden="True"/>
6884 <data name="OUTPUT_plink_king __make_king KING_robust" format="plink.king --make-king KING-robust" label="${tool.name} on ${on_string}: plink.king --make-king KING-robust" from_work_dir="plink.king --make-king KING-robust" hidden="True"/>
6885 <data name="OUTPUT_plink_legend __export" format="plink.legend --export" label="${tool.name} on ${on_string}: plink.legend --export" from_work_dir="plink.legend --export" hidden="True"/>
6886 <data name="OUTPUT_plink_normalized __normalize" format="plink.normalized --normalize" label="${tool.name} on ${on_string}: plink.normalized --normalize" from_work_dir="plink.normalized --normalize" hidden="True"/>
6887 <data name="OUTPUT_plink_pgen __make_[b]pgen PLINK" format="plink.pgen --make-[b]pgen PLINK" label="${tool.name} on ${on_string}: plink.pgen --make-[b]pgen PLINK" from_work_dir="plink.pgen --make-[b]pgen PLINK" hidden="True"/>
6888 <data name="OUTPUT_plink_prune_in __indep_pairwise Pruned" format="plink.prune.in --indep-pairwise Pruned" label="${tool.name} on ${on_string}: plink.prune.in --indep-pairwise Pruned" from_work_dir="plink.prune.in --indep-pairwise Pruned" hidden="True"/>
6889 <data name="OUTPUT_plink_prune_out __indep_pairwise IDs" format="plink.prune.out --indep-pairwise IDs" label="${tool.name} on ${on_string}: plink.prune.out --indep-pairwise IDs" from_work_dir="plink.prune.out --indep-pairwise IDs" hidden="True"/>
6890 <data name="OUTPUT_plink_psam __make_pgen___ PLINK" format="plink.psam --make-pgen... PLINK" label="${tool.name} on ${on_string}: plink.psam --make-pgen... PLINK" from_work_dir="plink.psam --make-pgen... PLINK" hidden="True"/>
6891 <data name="OUTPUT_plink_pvar __make_pgen___ PLINK" format="plink.pvar --make-pgen... PLINK" label="${tool.name} on ${on_string}: plink.pvar --make-pgen... PLINK" from_work_dir="plink.pvar --make-pgen... PLINK" hidden="True"/>
6892 <data name="OUTPUT_plink_raw __export" format="plink.raw --export" label="${tool.name} on ${on_string}: plink.raw --export" from_work_dir="plink.raw --export" hidden="True"/>
6893 <data name="OUTPUT_plink_recoverid_dup __recover_var_ids List" format="plink.recoverid.dup --recover-var-ids List" label="${tool.name} on ${on_string}: plink.recoverid.dup --recover-var-ids List" from_work_dir="plink.recoverid.dup --recover-var-ids List" hidden="True"/>
6894 <data name="OUTPUT_plink_rel __make_rel Relationship" format="plink.rel --make-rel Relationship" label="${tool.name} on ${on_string}: plink.rel --make-rel Relationship" from_work_dir="plink.rel --make-rel Relationship" hidden="True"/>
6895 <data name="OUTPUT_plink_rmdup_list __rm_dup" format="plink.rmdup.list --rm-dup" label="${tool.name} on ${on_string}: plink.rmdup.list --rm-dup" from_work_dir="plink.rmdup.list --rm-dup" hidden="True"/>
6896 <data name="OUTPUT_plink_rmdup_mismatch __rm_dup List" format="plink.rmdup.mismatch --rm-dup List" label="${tool.name} on ${on_string}: plink.rmdup.mismatch --rm-dup List" from_work_dir="plink.rmdup.mismatch --rm-dup List" hidden="True"/>
6897 <data name="OUTPUT_plink_sample __export Oxford" format="plink.sample --export Oxford" label="${tool.name} on ${on_string}: plink.sample --export Oxford" from_work_dir="plink.sample --export Oxford" hidden="True"/>
6898 <data name="OUTPUT_plink_scount __sample_counts Sample" format="plink.scount --sample-counts Sample" label="${tool.name} on ${on_string}: plink.scount --sample-counts Sample" from_work_dir="plink.scount --sample-counts Sample" hidden="True"/>
6899 <data name="OUTPUT_plink_sdiff __sample_diff Sample_pair" format="plink.sdiff --sample-diff Sample-pair" label="${tool.name} on ${on_string}: plink.sdiff --sample-diff Sample-pair" from_work_dir="plink.sdiff --sample-diff Sample-pair" hidden="True"/>
6900 <data name="OUTPUT_plink_sdiff_summary __sample_diff Sample_pair" format="plink.sdiff.summary --sample-diff Sample-pair" label="${tool.name} on ${on_string}: plink.sdiff.summary --sample-diff Sample-pair" from_work_dir="plink.sdiff.summary --sample-diff Sample-pair" hidden="True"/>
6901 <data name="OUTPUT_plink_smiss __missing Sample_based" format="plink.smiss --missing Sample-based" label="${tool.name} on ${on_string}: plink.smiss --missing Sample-based" from_work_dir="plink.smiss --missing Sample-based" hidden="True"/>
6902 <data name="OUTPUT_plink_snplist __write_snplist List" format="plink.snplist --write-snplist List" label="${tool.name} on ${on_string}: plink.snplist --write-snplist List" from_work_dir="plink.snplist --write-snplist List" hidden="True"/>
6903 <data name="OUTPUT_plink_sscore __score Sample" format="plink.sscore --score Sample" label="${tool.name} on ${on_string}: plink.sscore --score Sample" from_work_dir="plink.sscore --score Sample" hidden="True"/>
6904 <data name="OUTPUT_plink_traw __export" format="plink.traw --export" label="${tool.name} on ${on_string}: plink.traw --export" from_work_dir="plink.traw --export" hidden="True"/>
6905 <data name="OUTPUT_plink_vcf __export" format="plink.vcf --export" label="${tool.name} on ${on_string}: plink.vcf --export" from_work_dir="plink.vcf --export" hidden="True"/>
6906 <data name="OUTPUT_plink_vmiss __missing Variant_based" format="plink.vmiss --missing Variant-based" label="${tool.name} on ${on_string}: plink.vmiss --missing Variant-based" from_work_dir="plink.vmiss --missing Variant-based" hidden="True"/>
6907 <data name="OUTPUT_plink_vscore __variant_score Text" format="plink.vscore --variant-score Text" label="${tool.name} on ${on_string}: plink.vscore --variant-score Text" from_work_dir="plink.vscore --variant-score Text" hidden="True"/>
6908 <data name="OUTPUT_plink_vscore_bin __variant_score Binary" format="plink.vscore.bin --variant-score Binary" label="${tool.name} on ${on_string}: plink.vscore.bin --variant-score Binary" from_work_dir="plink.vscore.bin --variant-score Binary" hidden="True"/>
6909 <data name="OUTPUT_plink_vscore_cols __variant_score Column" format="plink.vscore.cols --variant-score Column" label="${tool.name} on ${on_string}: plink.vscore.cols --variant-score Column" from_work_dir="plink.vscore.cols --variant-score Column" hidden="True"/>
6910 <data name="OUTPUT_plink_vscore_vars __variant_score Variant" format="plink.vscore.vars --variant-score Variant" label="${tool.name} on ${on_string}: plink.vscore.vars --variant-score Variant" from_work_dir="plink.vscore.vars --variant-score Variant" hidden="True"/>
6911 <collection name="OUTPUT_plink___zst pack Zstd_compressed" type="list" label="plink.*.zst&#9;pack&#9;Zstd-compressed" hidden="True">
6912 <discover_datasets pattern="plink\.(?P&lt;name&gt;)\.zst\&#9;pack\&#9;Zstd\-compressed" format="plink.*.zst pack Zstd-compressed"/>
6913 </collection>
6914 <data name="OUTPUT_plink_log" format="plink.log" label="${tool.name} on ${on_string}: plink.log" from_work_dir="plink.log" hidden="False"/>
6915 </outputs>
6916 <help><![CDATA[
6917 ::
6918
6919 PLINK v2.00a2.3 AVX2 (24 Jan 2020) www.cog-genomics.org/plink/2.0/
6920 (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3
6921
6922 In the command line flag definitions that follow,
6923 * <angle brackets> denote a required parameter, where the text between the
6924 angle brackets describes its nature.
6925 * ['square brackets + single-quotes'] denotes an optional modifier. Use the
6926 EXACT text in the quotes.
6927 * [{bar|separated|braced|bracketed|values}] denotes a collection of mutually
6928 exclusive optional modifiers (again, the exact text must be used). When
6929 there are no outer square brackets, one of the choices must be selected.
6930 * ['quoted_text='<description of value>] denotes an optional modifier that
6931 must begin with the quoted text, and be followed by a value with no
6932 whitespace in between. '|' may also be used here to indicate mutually
6933 exclusive options.
6934 * [square brackets without quotes or braces] denote an optional parameter,
6935 where the text between the brackets describes its nature.
6936 * An ellipsis (...) indicates that you may enter multiple parameters of the
6937 specified type.
6938 * A "column set descriptor" is either
6939 1. a comma-separated sequence of column set names; this is interpreted as
6940 the full list of column sets to include.
6941 2. a comma-separated sequence of column set names, all preceded by '+' or
6942 '-'; this is interpreted as a list of changes to the default.
6943
6944 plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...]
6945 plink2 --help [flag name(s)...]
6946
6947 Most PLINK runs require exactly one main input fileset. The following flags
6948 are available for defining its form and location:
6949
6950 --pfile <prefix> ['vzs'] : Specify .pgen + .pvar[.zst] + .psam prefix.
6951 --pgen <filename> : Specify full name of .pgen/.bed file.
6952 --pvar <filename> : Specify full name of .pvar/.bim file.
6953 --psam <filename> : Specify full name of .psam/.fam file.
6954
6955 --bfile <prefix> ['vzs'] : Specify .bed + .bim[.zst] + .fam prefix.
6956 --bpfile <prefix> ['vzs'] : Specify .pgen + .bim[.zst] + .fam prefix.
6957
6958 --keep-autoconv : When importing non-PLINK-binary data, don't delete
6959 autogenerated binary fileset at end of run.
6960
6961 --no-fid : .fam file does not contain column 1 (family ID).
6962 --no-parents : .fam file does not contain columns 3-4 (parents).
6963 --no-sex : .fam file does not contain column 5 (sex).
6964
6965 --vcf <filename> ['dosage='<field>]
6966 --bcf <filename> ['dosage='<field>] (not implemented yet) :
6967 Specify full name of .vcf{|.gz|.zst} or BCF2 file to import.
6968 * These can be used with --psam/--fam.
6969 * By default, dosage information is not imported. To import the GP field
6970 (must be VCFv4.3-style 0..1, one probability per possible genotype), add
6971 'dosage=GP' (or 'dosage=GP-force', see below). To import Minimac3-style
6972 DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else
6973 for now) causes the named field to be interpreted as a Minimac3-style
6974 dosage.
6975 Note that, in the dosage=GP case, PLINK 2 collapses the probabilities
6976 down to dosages; you cannot use PLINK 2 to losslessly convert VCF
6977 FORMAT:GP data to e.g. BGEN format. To make this more obvious, PLINK 2
6978 now errors out when dosage=GP is used on a file with a FORMAT:DS header
6979 line and --import-dosage-certainty wasn't specified, since dosage=DS
6980 extracts the same information more quickly in this situation. You can
6981 suppress this error with 'dosage=GP-force'.
6982 In all of these cases, hardcalls are regenerated from scratch from the
6983 dosages. As a consequence, variants with no GT field can now be
6984 imported; they will be assumed to contain only diploid calls when HDS is
6985 also absent.
6986
6987 --data <filename prefix> [REF/ALT mode] ['gzs']
6988 --bgen <filename> [REF/ALT mode] ['snpid-chr']
6989 --gen <filename> [REF/ALT mode]
6990 --sample <filename> :
6991 Specify an Oxford-format dataset to import. --data specifies a .gen[.zst]
6992 + .sample pair, while --bgen specifies a BGEN v1.1+ file.
6993 * If a BGEN v1.2+ file contains sample IDs, it may be imported without a
6994 companion .sample file.
6995 * With 'snpid-chr', chromosome codes are read from the 'SNP ID' field
6996 instead of the usual chromosome field.
6997 * The following REF/ALT modes are supported:
6998 'ref-first': The first allele for each variant is REF.
6999 'ref-last': The last allele for each variant is REF.
7000 'ref-unknown' (default): The last allele for each variant is treated as
7001 provisional-REF.
7002 This parameter will be required instead of optional in alpha 3.
7003
7004 --haps <filename> [{ref-first | ref-last}]
7005 --legend <filename> <chr code> :
7006 Specify .haps [+ .legend] file(s) to import.
7007 * When --legend is specified, it's assumed that the --haps file doesn't
7008 contain header columns.
7009 * On chrX, the second male column may contain dummy '-' entries. (However,
7010 PLINK 2 currently cannot handle omitted male columns.)
7011 * If not used with --sample, new sample IDs are of the form 'per#/per#'.
7012
7013 --map <filename> : Specify full name of .map file.
7014 --import-dosage <allele dosage file> ['noheader'] ['id-delim='<char>]
7015 ['skip0='<i>] ['skip1='<j>] ['skip2='<k>] ['dose1']
7016 ['format='<m>] [{ref-first | ref-last}]
7017 ['single-chr='<code>] ['chr-col-num='<#>]
7018 ['pos-col-num='<#>] :
7019 Specify PLINK 1.x-style dosage file to import.
7020 * You must also specify a companion .psam/.fam file.
7021 * By default, PLINK assumes that the file contains a header line, which has
7022 'SNP' in (1-based) column i+1, 'A1' in column i+j+2, 'A2' in column
7023 i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are
7024 normally zero, but can be changed with 'skip0', 'skip1', and 'skip2'
7025 respectively. FID/IID are normally assumed to be separate tokens, but if
7026 they're merged into a single token you can specify the delimiter with
7027 'id-delim='.) If such a header line is not present, use the 'noheader'
7028 modifier; samples will then be assumed to appear in the same order as
7029 they do in the .psam/.fam file.
7030 * You may specify a companion .map file. If you do not,
7031 * 'single-chr=' can be used to specify that all variants are on the named
7032 chromosome. Otherwise, you can use 'chr-col-num=' to read chromosome
7033 codes from the given (1-based) column number.
7034 * 'pos-col-num=' causes bp coordinates to be read from the given column
7035 number.
7036 * The 'format=' modifier lets you specify the number of values used to
7037 represent each dosage. 'format=1' normally indicates a single 0..2 A1
7038 expected count; 'dose1' modifies this to a 0..1 frequency. 'format=2'
7039 indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het
7040 likelihood. 'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2.
7041 'format=infer' (the default) infers the format from the number of columns
7042 in the first nonheader line.
7043
7044 --dummy <sample ct> <SNP ct> [missing dosage freq] [missing pheno freq]
7045 [{acgt | 1234 | 12}] ['pheno-ct='<count>] ['scalar-pheno']
7046 ['dosage-freq='<rate>]
7047 This generates a fake input dataset with the specified number of samples
7048 and SNPs.
7049 * By default, the missing dosage and phenotype frequencies are zero.
7050 These can be changed by providing 3rd and 4th numeric parameters.
7051 * By default, allele codes are As and Bs; this can be changed with the
7052 'acgt', '1234', or '12' modifier.
7053 * By default, one binary phenotype is generated. 'pheno-ct=' can be used
7054 to change the number of phenotypes, and 'scalar-pheno' causes these
7055 phenotypes to be normally distributed scalars.
7056 * By default, all (nonmissing) dosages are in {0,1,2}. To make some of
7057 them take on decimal values, use 'dosage-freq='. (These dosages are
7058 affected by --hard-call-threshold and --dosage-erase-threshold.)
7059
7060 --fa <filename> : Specify full name of reference FASTA file.
7061
7062 Output files have names of the form 'plink2.<extension>' by default. You can
7063 change the 'plink2' prefix with
7064
7065 --out <prefix> : Specify prefix for output files.
7066
7067 Most runs also require at least one of the following commands:
7068
7069 --rm-dup [mode] ['list']
7070 Remove all but one instance of each duplicate-ID variant (ignoring the
7071 missing ID), and (with the 'list' modifier) write a list of duplicated IDs
7072 to <output prefix>.rmdup.list.
7073 The following modes of operation are supported:
7074 * 'error' (default) causes this to error out when there's a genotype data
7075 or other mismatch between the records. A list of affected IDs is written
7076 to <output prefix>.rmdup.mismatch.
7077 * 'retain-mismatch' causes all instances of a duplicate-ID variant to be
7078 retained when there's a genotype data or variant info mismatch; otherwise
7079 one instance is kept. The .rmdup.mismatch file is also written.
7080 * 'exclude-mismatch' removes all instances of duplicate-ID mismatched
7081 variants instead.
7082 * 'exclude-all' causes all instances of duplicate-ID variants to be
7083 removed, even when the actual records are identical.
7084 * 'force-first' causes only the first instance of duplicate-ID variants to
7085 be kept, under all circumstances.
7086
7087 --make-pgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase']
7088 ['erase-dosage'] ['pvar-cols='<col set descriptor>]
7089 ['psam-cols='<col set descriptor>]
7090 --make-bpgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase']
7091 ['erase-dosage']
7092 --make-bed ['vzs'] ['trim-alts']
7093 Create a new PLINK binary fileset (--make-pgen = .pgen + .pvar[.zst] +
7094 .psam, --make-bpgen = .pgen + .bim[.zst] + .fam).
7095 * Unlike the automatic text-to-binary converters (which only heed
7096 chromosome filters), this supports all of PLINK's filtering flags.
7097 * The 'vzs' modifier causes the variant file (.pvar/.bim) to be
7098 Zstd-compressed.
7099 * The 'format' modifier requests an uncompressed fixed-variant-width .pgen
7100 file. (These do not directly support multiallelic variants.) The
7101 following format code is currently supported:
7102 2: just like .bed, except with an extended (12-byte instead of 3-byte)
7103 header containing variant/sample counts, and rotated genotype codes
7104 (00 = hom ref, 01 = het, 10 = hom alt, 11 = missing).
7105 * The 'erase-phase' and 'erase-dosage' modifiers prevent phase and dosage
7106 information from being written to the new .pgen.
7107 * The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT.
7108 Supported optional .pvar column sets are:
7109 xheader: All ## header lines (yeah, this is technically not a column),
7110 except for possibly FILTER/INFO definitions when those
7111 column(s) have been removed. Without this, only the #CHROM
7112 header line is kept.
7113 maybequal: QUAL. Omitted if all remaining values are missing.
7114 qual: Force QUAL column to be written even when empty.
7115 maybefilter: FILTER. Omitted if all remaining values are missing.
7116 filter: Force FILTER column to be written even when empty.
7117 maybeinfo: INFO. Omitted if all remaining values are missing, or if
7118 INFO:PR is the only subfield.
7119 info: Force INFO column to be written.
7120 maybecm: Centimorgan coordinate. Omitted if all remaining values = 0.
7121 cm: Force CM column to be written even when empty.
7122 The default is xheader,maybequal,maybefilter,maybeinfo,maybecm.
7123 * Supported column sets for the .psam file are:
7124 maybefid: Family ID, '0' = missing. Omitted if all values missing.
7125 fid: Force FID column to be written even when empty.
7126 maybesid: Source ID, '0' = missing. Omitted if all values missing.
7127 sid: Force SID column to be written even when empty.
7128 maybeparents: Father and mother IIDs. Omitted if all values missing.
7129 parents: Force PAT and MAT columns to be written even when empty.
7130 sex: '1' = male, '2' = female, 'NA' = missing.
7131 pheno1: First active phenotype. If none, all column entries are set to
7132 the --output-missing-phenotype string.
7133 phenos: All active phenotypes, if any. (Can be combined with pheno1 to
7134 force at least one phenotype column to be written.)
7135 The default is maybefid,maybesid,maybeparents,sex,phenos.
7136
7137 --make-just-pvar ['zs'] ['cols='<column set descriptor>]
7138 --make-just-psam ['cols='<column set descriptor>]
7139 --make-just-bim ['zs']
7140 --make-just-fam
7141 Variants of --make-pgen/--make-bed which only write a new variant or sample
7142 file. These don't always require an input genotype file.
7143 USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary
7144 genotype data and your sample/variant indexes if you use these commands
7145 improperly. If you have any doubt, stick with --make-[b]pgen/--make-bed.
7146
7147 --export <output format(s)...> [{01 | 12}] ['bgz'] ['id-delim='<char>]
7148 ['id-paste='<column set descriptor>] ['include-alt']
7149 ['omit-nonmale-y'] ['spaces'] ['vcf-dosage='<field>] ['ref-first']
7150 ['bits='<#>]
7151 Create a new fileset with all filters applied. The following output
7152 formats are supported:
7153 (actually, only A, AD, A-transpose, bgen-1.x, ind-major-bed, haps,
7154 hapslegend, oxford, and vcf are implemented for now)
7155 * '23': 23andMe 4-column format. This can only be used on a single
7156 sample's data (--keep may be handy), and does not support
7157 multicharacter allele codes.
7158 * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R.
7159 If you need uncounted alleles to be named in the header line, add
7160 the 'include-alt' modifier.
7161 * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding.
7162 Also supports 'include-alt'.
7163 * 'A-transpose': Variant-major 0/1/2.
7164 * 'beagle': Unphased per-autosome .dat and .map files, readable by early
7165 BEAGLE versions.
7166 * 'beagle-nomap': Single .beagle.dat file.
7167 * 'bgen-1.x': Oxford-format .bgen + .sample. For v1.2/v1.3, sample
7168 identifiers are stored in the .bgen (with id-delim and
7169 id-paste settings applied), and default precision is 16-bit
7170 (use the 'bits' modifier to reduce this).
7171 * 'bimbam': Regular BIMBAM format.
7172 * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file. Does not
7173 support multiple chromosomes.
7174 * 'fastphase': Per-chromosome fastPHASE files, with
7175 .chr-<chr #>.phase.inp filename extensions.
7176 * 'fastphase-1chr': Single .phase.inp file. Does not support
7177 multiple chromosomes.
7178 * 'haps', 'hapslegend': Oxford-format .haps + .sample[ + .legend]. All
7179 data must be biallelic and phased. When the 'bgz'
7180 modifier is present, the .haps file is
7181 block-gzipped.
7182 * 'HV': Per-chromosome Haploview files, with .chr-<chr #>{.ped,.info}
7183 filename extensions.
7184 * 'HV-1chr': Single Haploview .ped + .info file pair. Does not support
7185 multiple chromosomes.
7186 * 'ind-major-bed': PLINK 1 sample-major .bed (+ .bim + .fam).
7187 * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile.
7188 * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile +
7189 --reference.
7190 * 'list': Single genotype-based list, up to 4 lines per variant. To omit
7191 nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y'
7192 modifier.
7193 * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a
7194 genotype-based list which omits the most common genotype for
7195 each variant. Also supports 'omit-nonmale-y'.
7196 * 'oxford': Oxford-format .gen + .sample. When the 'bgz' modifier is
7197 present, the .gen file is block-gzipped.
7198 * 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file.
7199 * 'compound-genotypes': Same as 'ped', except that the space between each
7200 pair of same-variant allele codes is removed.
7201 * 'structure': Structure-format.
7202 * 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with
7203 --tfile.
7204 * 'vcf', 'vcf-4.2': VCF (default version 4.3). If PAR1 and PAR2 are
7205 present, they are automatically merged with chrX, with
7206 proper handling of chromosome codes and male ploidy.
7207 When the 'bgz' modifier is present, the VCF file is
7208 block-gzipped.
7209 The 'id-paste' modifier controls which .psam columns
7210 are used to construct sample IDs (choices are maybefid,
7211 fid, iid, maybesid, and sid; default is
7212 maybefid,iid,maybesid), while the 'id-delim' modifier
7213 sets the character between the ID pieces (default '_').
7214 Dosages are not exported unless the 'vcf-dosage='
7215 modifier is present. The following five dosage export
7216 modes are supported:
7217 'GP': genotype posterior probabilities (v4.3 only).
7218 'DS': Minimac3-style dosages, omitted for hardcalls.
7219 'DS-force': Minimac3-style dosages, never omit.
7220 'HDS': Minimac3-style phased dosages, omitted for
7221 hardcalls and unphased calls. Also includes
7222 'DS' output.
7223 'HDS-force': Always report DS and HDS.
7224 In addition,
7225 * The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles
7226 to be coded as '2', while '01' maps alt1 -> 0 and ref -> 1.
7227 * The 'spaces' modifier makes the output space-delimited instead of
7228 tab-delimited, whenever both are permitted.
7229 * For biallelic formats where it's unspecified whether the reference/major
7230 allele should appear first or second, --export defaults to second for
7231 compatibility with PLINK 1.9. Use 'ref-first' to change this.
7232 (Note that this doesn't apply to the 'A', 'AD', and 'A-transpose'
7233 formats; use --export-allele to control which alleles are counted there.)
7234
7235 --freq ['zs'] ['counts'] ['cols='<column set descriptor>] ['bins-only']
7236 ['refbins='<comma-separated bin boundaries> | 'refbins-file='<file>]
7237 ['alt1bins='<comma-separated bin boundaries> | 'alt1bins-file='<file>]
7238 Empirical allele frequency report. By default, only founders are
7239 considered. Dosages are taken into account (e.g. heterozygous haploid
7240 calls count as 0.5).
7241 Supported column sets are:
7242 chrom: Chromosome ID.
7243 pos: Base-pair coordinate.
7244 (ID is always present, and positioned here.)
7245 ref: Reference allele.
7246 alt1: Alternate allele 1.
7247 alt: All alternate alleles, comma-separated.
7248 reffreq: Reference allele frequency/dosage.
7249 alt1freq: Alt1 frequency/dosage.
7250 altfreq: Comma-separated frequencies/dosages for all alternate alleles.
7251 freq: Similar to altfreq, except ref is also included at the start.
7252 eq: Comma-separated <allele>=<freq> for all present alleles. (If no
7253 alleles are present, the column contains a single '.'.)
7254 eqz: Same as eq, except zero-counts are included.
7255 alteq/alteqz: Same as eq/eqz, except reference allele is omitted.
7256 numeq: 0=<freq>,1=<freq>, etc. Zero-counts are omitted.
7257 altnumeq: Same as numeq, except reference allele is omitted.
7258 machr2: Unphased MaCH imputation quality metric.
7259 minimac3r2: Phased Minimac3 imputation quality.
7260 nobs: Number of allele observations.
7261 The default is chrom,ref,alt,altfreq,nobs.
7262 Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with
7263 'counts') file(s) are generated when 'refbins='/'refbins-file=' or
7264 'alt1bins='/'alt1bins-file=' is present; these report the total number of
7265 frequencies or counts in each left-closed, right-open interval. (If you
7266 only want these histogram(s), and not the main report, add 'bins-only'.)
7267
7268 --geno-counts ['zs'] ['cols='<column set descriptor>]
7269 Variant-based hardcall genotype count report (considering both alleles
7270 simultaneously in the diploid case). Nonfounders are now included; use
7271 --keep-founders if this is a problem. Heterozygous haploid calls are
7272 treated as missing.
7273 Supported column sets are:
7274 chrom: Chromosome ID.
7275 pos: Base-pair coordinate.
7276 (ID is always present, and positioned here.)
7277 ref: Reference allele.
7278 alt1: Alternate allele 1.
7279 alt: All alternate alleles, comma-separated.
7280 homref: Homozygous-ref count.
7281 refalt1: Heterozygous ref-alt1 count.
7282 refalt: Comma-separated het ref-altx counts.
7283 homalt1: Homozygous-alt1 count.
7284 altxy: Comma-separated altx-alty counts, in (1/1)-(1/2)-(2/2)-(1/3)-...
7285 order.
7286 xy: Similar to altxy, except the reference allele is treated as alt0,
7287 and the sequence starts (0/0)-(0/1)-(1/1)-(0/2)-...
7288 hapref: Haploid-ref count.
7289 hapalt1: Haploid-alt1 count.
7290 hapalt: Comma-separated haploid-altx counts.
7291 hap: Similar to hapalts, except ref is also included at the start.
7292 numeq: 0/0=<hom ref ct>,0/1=<het ref-alt1>,1/1=<hom alt1>,...,0=<hap ref>
7293 etc. Zero-counts are omitted. (If all genotypes are missing, the
7294 column contains a single '.'.)
7295 missing: Number of missing genotypes.
7296 nobs: Number of (nonmissing) genotype observations.
7297 The default is chrom,ref,alt,homref,refalt,altxy,hapref,hapalt,missing.
7298
7299 --sample-counts ['zs'] ['cols='<column set descriptor>]
7300 Sample-based hardcall genotype count report.
7301 * Unknown-sex samples are treated as female.
7302 * Heterozygous haploid calls (MT included) are treated as missing.
7303 * As with other PLINK 2 commands, SNPs that have not been left-normalized
7304 are counted as non-SNP non-symbolic. (Use e.g. --normalize when that's a
7305 problem.)
7306 * Supported column sets are:
7307 maybefid: FID, if that column was present in the input.
7308 fid: Force FID column to be written even when absent in the input.
7309 (IID is always present, and positioned here.)
7310 maybesid: SID, if that column was present in the input.
7311 sid: Force SID column to be written even when absent in the input.
7312 sex: '1' = male, '2' = female, 'NA' = missing.
7313 hom: Homozygous genotype count.
7314 homref: Homozygous-ref genotype count.
7315 homalt: Homozygous-alt genotype count.
7316 homaltsnp: Homozygous-alt SNP count.
7317 het: Heterozygous genotype count.
7318 refalt: Heterozygous ref-altx genotype count.
7319 het2alt: Heterozygous altx-alty genotype count.
7320 hetsnp: Heterozygous SNP count.
7321 dipts: Diploid SNP transition count.
7322 ts: SNP transition count (excluding chrY for females).
7323 diptv: Diploid SNP transversion count.
7324 tv: SNP transversion count.
7325 dipnonsnpsymb: Diploid non-SNP, non-symbolic count.
7326 nonsnpsymb: Non-SNP, non-symbolic count.
7327 symbolic: Symbolic variant count.
7328 nonsnp: Non-SNP count.
7329 dipsingle: Number of singletons relative to this dataset, across just
7330 diploid calls. (Note that if the ALT allele in a chrX
7331 biallelic variant appears in exactly one female and one
7332 male, that counts as a singleton for just the female.)
7333 single: Number of singletons relative to this dataset.
7334 haprefwfemaley: Haploid-ref count, counting chrY for everyone.
7335 hapref: Haploid-ref count, excluding chrY for females.
7336 hapaltwfemaley: Haploid-alt count, counting chrY for everyone.
7337 hapalt: Haploid-alt count, excluding chrY for females.
7338 missingwfemaley: Missing call count, counting chrY for everyone.
7339 missing: Missing call count, excluding chrY for females.
7340 The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv,
7341 dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley.
7342 * The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb',
7343 'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous
7344 altx-alty call separately, since they can be of different subtypes.
7345 (I.e. if they are of the same subtype, the corresponding count is
7346 incremented by 2.) As a consequence, these columns are unaffected by
7347 variant split/join.
7348
7349 --missing ['zs'] [{sample-only | variant-only}]
7350 ['scols='<column set descriptor>] ['vcols='<column set descriptor>]
7351 Generate sample- and variant-based missing data reports (or just one report
7352 if 'sample-only'/'variant-only' is specified).
7353 As of alpha 2, mixed MT hardcalls appear in the heterozygous haploid stats.
7354 Supported column sets in the sample-based report are:
7355 maybefid: FID, if that column was present in the input.
7356 fid: Force FID column to be written even when absent in the input.
7357 (IID is always present, and positioned here.)
7358 maybesid: SID, if that column was present in the input.
7359 sid: Force SID column to be written even when absent in the input.
7360 misspheno1: First active phenotype missing (Y/N)? Always 'Y' if no
7361 phenotypes are loaded.
7362 missphenos: A Y/N column for each loaded phenotype. (Can be combined
7363 with misspheno1 to force at least one such column.)
7364 nmissdosage: Number of missing dosages.
7365 nmiss: Number of missing hardcalls, not counting het haploids.
7366 nmisshh: Number of missing hardcalls, counting het haploids.
7367 hethap: Number of heterozygous haploid hardcalls.
7368 nobs: Denominator (male count on chrY, otherwise total sample count).
7369 fmissdosage: Missing dosage rate.
7370 fmiss: Missing hardcall rate, not counting het haploids.
7371 fmisshh: Missing hardcall rate, counting het haploids.
7372 The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss.
7373 Supported column sets in the variant-based report are:
7374 chrom: Chromosome ID.
7375 pos: Base-pair coordinate.
7376 (ID is always present, and positioned here.)
7377 ref: Reference allele.
7378 alt1: Alternate allele 1.
7379 alt: All alternate alleles, comma-separated.
7380 nmissdosage: Number of missing dosages.
7381 nmiss: Number of missing hardcalls, not counting het haploids.
7382 nmisshh: Number of missing hardcalls, counting het haploids.
7383 hethap: Number of heterozygous haploid calls.
7384 nobs: Number of potentially valid calls.
7385 fmissdosage: Missing dosage rate.
7386 fmiss: Missing hardcall rate, not counting het haploids.
7387 fmisshh: Missing hardcall rate, counting het haploids.
7388 fhethap: Heterozygous haploid rate.
7389 The default is chrom,nmiss,nobs,fmiss.
7390
7391 --hardy ['zs'] ['midp'] ['redundant'] ['cols='<column set descriptor>]
7392 Hardy-Weinberg exact test p-value report(s).
7393 * By default, only founders are considered; change this with --nonfounders.
7394 * chrX is now omitted from the main <output prefix>.hardy report. Instead,
7395 (if present) it gets its own <output prefix>.hardy.x report based on the
7396 method described in Graffelman J, Weir BS (2016) Hardy-Weinberg
7397 equilibrium and the X chromosome.
7398 * For variants with k alleles where k>2, k separate 'biallelic' tests are
7399 performed, each reported on its own line. However, biallelic variants
7400 are normally reported on a single line, since the counts/frequencies
7401 would be mirror-images and the p-values would be the same. You can add
7402 the 'redundant' modifier to force biallelic variant results to be
7403 reported on two lines for parsing convenience.
7404 * There is currently no special handling of case/control phenotypes.
7405 Supported column sets are:
7406 chrom: Chromosome ID.
7407 pos: Base-pair coordinate.
7408 (ID is always present, and positioned here.)
7409 ref: Reference allele.
7410 alt1: Alternate allele 1.
7411 alt: All alternate alleles, comma-separated.
7412 (A1 is always present, and positioned here.)
7413 ax: Non-A1 allele(s), comma-separated.
7414 gcounts: Hom-A1 count, total number of het-A1 calls, and total number of
7415 nonmissing calls with no copies of A1. On chrX, these are
7416 followed by male A1 and male non-A1 counts.
7417 gcount1col: gcounts values in a single comma-separated column.
7418 hetfreq: Observed and expected het-A1 frequencies.
7419 sexaf: Female and male A1 observed allele frequencies (chrX only).
7420 femalep: Female-only p/midp-value (chrX only).
7421 p: Hardy-Weinberg equilibrium exact test p/midp-value.
7422 The default is chrom,ax,gcounts,hetfreq,sexaf,p.
7423
7424 --indep-pairwise <window size>['kb'] [step size (variant ct)]
7425 <unphased-hardcall-r^2 threshold>
7426 Generate a list of variants in approximate linkage equilibrium.
7427 * For multiallelic variants, major allele counts are used in the r^2
7428 computation.
7429 * With the 'kb' modifier, the window size is in kilobase instead of variant
7430 count units. (Pre-'kb' space is optional, i.e.
7431 "--indep-pairwise 500 kb 0.5" and "--indep-pairwise 500kb 0.5" have the
7432 same effect.)
7433 * The step size now defaults to 1 if it's unspecified, and *must* be 1 if
7434 the window is in kilobase units.
7435 * Note that you need to rerun PLINK using --extract or --exclude on the
7436 .prune.in/.prune.out file to apply the list to another computation... and
7437 as with other applications of --extract/--exclude, duplicate variant IDs
7438 are a problem. --indep-pairwise still runs to completion for now when
7439 duplicate variant IDs are present, but that will become an error in alpha
7440 3.
7441
7442 --ld <variant ID> <variant ID> ['dosage'] ['hwe-midp']
7443 This displays diplotype frequencies, r^2, and D' for a single pair of
7444 variants.
7445 * For multiallelic variants, major allele counts/dosages are used.
7446 * Phase information is used when both variants are on the same chromosome.
7447 * When there is at least one sample with unphased het calls for both
7448 variants, diplotype frequencies are estimated using the Hill equation.
7449 If there are multiple biologically possible local maxima, all are
7450 displayed, along with HWE exact test statistics.
7451 * By default, only hardcalls are considered. Add the 'dosage' modifier if
7452 you want dosages to be taken into account. (In the diploid case, an
7453 unphased dosage of x is interpreted as P(0/0) = 1 - x, P(0/1) = x when x
7454 is in 0..1.)
7455
7456 --sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>]
7457 ['include-missing'] [{pairwise | counts-only}]
7458 ['fname-id-delim='<c>] ['zs'] ['cols='<column set descriptor>]
7459 ['counts-cols='<column set descriptor>]
7460 {base= | ids=}<sample ID> [other sample ID(s)...]
7461 --sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>]
7462 ['include-missing'] [{pairwise | counts-only}]
7463 ['fname-id-delim='<c>] ['zs'] ['cols='<column set descriptor>]
7464 ['counts-cols='<column set descriptor>] file=<ID-pair file>
7465 (alias: --sdiff)
7466 Report discordances and discordance-counts between pairs of samples. If
7467 chrX or chrY is present, sex must be defined and consistent.
7468 * There are three ways to specify which sample pairs to compare. To
7469 compare a single baseline sample against some others, start the
7470 (space-delimited) sample ID list with 'base='. To perform an all-vs.-all
7471 comparison, start it with 'ids=' instead. To compare sample pairs listed
7472 in a file, use 'file='.
7473 Note that 'base='/'ids='/'file=' must be positioned after all modifiers.
7474 * Sample IDs are interpreted as if they were in a VCF header line, with
7475 'id-delim=' having the usual effect.
7476 * By default, comparisons are based on hardcalls. Use 'dosage' to compare
7477 dosages instead; you can combine this with a tolerance in [0, 0.5).
7478 * By default, if one genotype is missing and the other isn't, that doesn't
7479 count as a difference; this can be changed with 'include-missing'.
7480 * By default, a single main report is written to
7481 <output prefix>[.<base ID>].sdiff. To write separate pairwise
7482 <output prefix>.<ID1>.<ID2>.sdiff reports for each compared ID pair, add
7483 the 'pairwise' modifier. To omit the main report, add the 'counts-only'
7484 modifier. (Note that, if you're only interested in nonmissing autosomal
7485 biallelic hardcalls, --make-king-table provides a more efficient way to
7486 compute just counts.)
7487 * By default, if an output filename has a multipart sample ID, the parts
7488 will be delimited by '_'; use 'fname-id-delim=' to change this.
7489 Supported main-report column sets are:
7490 chrom: Chromosome ID.
7491 pos: Base-pair coordinate.
7492 (Variant ID is always present, and positioned here.)
7493 ref: Reference allele.
7494 alt: All alternate alleles, comma-separated.
7495 maybefid: FID1/FID2, if that column was in the input. Requires 'id'.
7496 fid: Force FID1/FID2 even when FID was absent in the input.
7497 id: IID1/IID2.
7498 maybesid: SID1/SID2, if that column was in the input. Requires 'id'.
7499 sid: Force SID1/SID2 even when SID was absent in the input.
7500 geno: Unphased GT or DS for the two samples.
7501 The default is usually chrom,pos,ref,alt,maybefid,id,maybesid,geno; the
7502 sample IDs are removed from the default in 'pairwise' mode.
7503 Supported discordance-count-summary column sets are:
7504 maybefid: FID1/FID2, if that column was in the input.
7505 fid: Force FID1/FID2 even when FID was absent in the input.
7506 (IID1/IID2 are always present.)
7507 maybesid: SID1/SID2, if that column was in the input.
7508 sid: Force SID1/SID2 even when SID was absent in the input.
7509 nobs: Number of variants considered. This includes variants where one or
7510 both variants are missing iff 'include-missing' was specified.
7511 nobsibs: ibs0+ibs1+ibs2.
7512 ibs0: Number of diploid variants with no common hardcall alleles.
7513 ibs1: Number of diploid variants with exactly 1 common hardcall allele.
7514 ibs2: Number of diploid variants with both hardcall alleles matching.
7515 halfmiss: Number of variants with exactly 1 missing genotype/dosage.
7516 Ignored without 'include-missing'.
7517 diff: Total number of differences.
7518 The default is maybefid,maybesid,nobs,halfmiss,diff.
7519
7520 --make-king [{square | square0 | triangle}] [{zs | bin | bin4}]
7521 KING-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC,
7522 Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in
7523 genome-wide association studies. By default, this writes a
7524 lower-triangular tab-delimited table of kinship coefficients to
7525 <output prefix>.king, and a list of the corresponding sample IDs to
7526 <output prefix>.king.id. The first row of the .king file contains a single
7527 <genome 1-genome 2> kinship coefficient, the second row has the
7528 <genome 1-genome 3> and <genome 2-genome 3> kinship values in that order,
7529 etc.
7530 * Only autosomes are currently considered.
7531 * Pedigree information is currently ignored; the between-family estimator
7532 is used for all pairs.
7533 * For multiallelic variants, REF allele counts are used.
7534 * If the 'square' or 'square0' modifier is present, a square matrix is
7535 written instead; 'square0' fills the upper right triangle with zeroes.
7536 * If the 'zs' modifier is present, the .king file is Zstd-compressed.
7537 * If the 'bin' modifier is present, a binary (square) matrix of
7538 double-precision floating point values, suitable for loading from R, is
7539 instead written to <output prefix>.king.bin. ('bin4' specifies
7540 single-precision numbers instead.) This can be combined with 'square0'
7541 if you still want the upper right zeroed out, or 'triangle' if you don't
7542 want to pad the upper right at all.
7543 * The computation can be subdivided with --parallel.
7544 --make-king-table ['zs'] ['counts'] ['rel-check'] ['cols='<col set descrip.>]
7545 Similar to --make-king, except results are reported in KING's original
7546 .kin0 text table format (with minor changes, e.g. row order is more
7547 friendly to incremental addition of samples), --king-table-filter can be
7548 used to restrict the report to high kinship values, and the 'rel-check'
7549 modifier can be used to restrict to same-FID pairs.
7550 Supported column sets are:
7551 maybefid: FID1/FID2, if that column was in the input. Requires 'id'.
7552 fid: Force FID1/FID2 even when FID was absent in the input.
7553 id: IID1/IID2 (column headers are actually 'ID1'/'ID2' to match KING).
7554 maybesid: SID1/SID2, if that column was in the input. Requires 'id'.
7555 sid: Force SID1/SID2 even when SID was absent in the input.
7556 nsnp: Number of variants considered (autosomal, neither call missing).
7557 hethet: Proportion/count of considered call pairs which are het-het.
7558 ibs0: Proportion/count of considered call pairs which are opposite homs.
7559 ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts.
7560 kinship: KING-robust between-family kinship estimator.
7561 The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship.
7562 hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is
7563 present. If id is omitted, a .kin0.id file is also written.
7564
7565 --make-rel ['cov'] ['meanimpute'] [{square | square0 | triangle}]
7566 [{zs | bin | bin4}]
7567 Write a lower-triangular variance-standardized relationship matrix to
7568 <output prefix>.rel, and corresponding IDs to <output prefix>.rel.id.
7569 * This computation assumes that variants do not have very low MAF, or
7570 deviate greatly from Hardy-Weinberg equilibrium.
7571 * Also, it's usually best to perform this calculation on a variant set in
7572 approximate linkage equilibrium.
7573 * The 'cov' modifier replaces the variance-standardization step with basic
7574 mean-centering, causing a covariance matrix to be calculated instead.
7575 * The computation can be subdivided with --parallel.
7576 --make-grm-list ['cov'] ['meanimpute'] ['zs'] [{id-header | iid-only}]
7577 --make-grm-bin ['cov'] ['meanimpute'] [{id-header | iid-only}]
7578 --make-grm-list causes the relationships to be written to GCTA's original
7579 list format, which describes one pair per line, while --make-grm-bin writes
7580 them in GCTA 1.1+'s single-precision triangular binary format. Note that
7581 these formats explicitly report the number of valid observations (where
7582 neither sample has a missing call) for each pair, which is useful input for
7583 some scripts.
7584
7585 --pca [count] [{approx | meanimpute}] ['scols='<col set descriptor>]
7586 --pca [{biallelic-var-wts | var-wts}] [count] [{approx | meanimpute}] ['vzs']
7587 ['scols='<col set descriptor>] ['vcols='<col set descriptor>]
7588 Extracts top principal components from the variance-standardized
7589 relationship matrix.
7590 * It is usually best to perform this calculation on a variant set in
7591 approximate linkage equilibrium, with no very-low-MAF variants.
7592 * By default, 10 PCs are extracted; you can adjust this by passing a
7593 numeric parameter. (Note that 10 is lower than the PLINK 1.9 default of
7594 20; this is due to the randomized algorithm's memory footprint growing
7595 quadratically w.r.t. the PC count.)
7596 * The 'approx' modifier causes the standard deterministic computation to be
7597 replaced with the randomized algorithm originally implemented for
7598 Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ,
7599 Price AL (2016) Fast Principal-Component Analysis Reveals Convergent
7600 Evolution of ADH1B in Europe and East Asia. This can be a good idea when
7601 you have >5k samples.
7602 * The randomized algorithm always uses mean imputation for missing genotype
7603 calls. For comparison purposes, you can use the 'meanimpute' modifier to
7604 request this behavior for the standard computation.
7605 * 'scols=' can be used to customize how sample IDs appear in the .eigenvec
7606 file. (maybefid, fid, maybesid, and sid supported; default is
7607 maybefid,maybesid.)
7608 * The 'biallelic-var-wts' modifier requests an additional
7609 one-line-per-variant .eigenvec.var file with PCs expressed as variant
7610 weights instead of sample weights, with the condition that all variants
7611 must be biallelic. When it's present, 'vzs' causes the .eigenvec.var
7612 file to be Zstd-compressed.
7613 'vcols=' can be used to customize the report columns; supported column
7614 sets are:
7615 chrom: Chromosome ID.
7616 pos: Base-pair coordinate.
7617 (ID is always present, and positioned here.)
7618 ref: Reference allele.
7619 alt1: Alternate allele 1.
7620 alt: All alternate alleles, comma-separated.
7621 maj: Major allele.
7622 nonmaj: All nonmajor alleles, comma-separated.
7623 (PCs are always present, and positioned here. Signs are w.r.t. the
7624 major, not necessarily reference, allele.)
7625 Default is chrom,maj,nonmaj.
7626 * In this build, 'var-wts' generates the same report as biallelic-var-wts,
7627 except with the "all variants must be biallelic" restriction lifted.
7628 This is temporary. It will no longer be supported as of alpha 3;
7629 instead, there will be an 'allele-wts' mode which seamlessly handles
7630 multiallelic variants, at the cost of generating more verbose
7631 one-line-per-allele output.
7632
7633 --king-cutoff [.king.bin + .king.id fileset prefix] <threshold>
7634 Exclude one member of each pair of samples with KING-robust kinship greater
7635 than the given threshold. Remaining/excluded sample IDs are written to
7636 <output prefix>.king.cutoff.in.id + .king.cutoff.out.id.
7637 If present, the .king.bin file must be triangular (either precision is ok).
7638
7639 --write-covar ['cols='<column set descriptor>]
7640 If covariates are defined, an updated version (with all filters applied) is
7641 automatically written to <output prefix>.cov whenever --make-pgen,
7642 --make-just-psam, --export, or a similar command is present. However, if
7643 you do not wish to simultaneously generate a new sample file, you can use
7644 --write-covar to just produce a pruned covariate file.
7645 Supported column sets are:
7646 maybefid: FID, if that column was in the input.
7647 fid: Force FID column to be written even when absent in the input.
7648 maybesid: SID, if that column was in the input.
7649 sid: Force SID column to be written even when absent in the input.
7650 maybeparents: Father/mother IIDs ('0' = missing), if columns in input.
7651 parents: Force PAT/MAT columns to be written even when absent in input.
7652 sex: '1' = male, '2' = female, 'NA' = missing.
7653 pheno1: First active phenotype. If none, all column entries are set to
7654 the --output-missing-phenotype string.
7655 phenos: All active phenotypes, if any. (Can be combined with pheno1 to
7656 force at least one phenotype column to be written.)
7657 (Covariates are always present, and positioned here.)
7658 The default is maybefid,maybesid.
7659
7660 --write-samples
7661 Report IDs of all samples which pass your filters/inclusion thresholds.
7662
7663 --write-snplist ['zs']
7664 List all variants which pass your filters/inclusion thresholds.
7665
7666 --glm ['zs'] ['omit-ref'] [{sex | no-x-sex}] ['log10'] ['pheno-ids']
7667 [{genotypic | hethom | dominant | recessive}] ['interaction']
7668 ['hide-covar'] ['intercept'] [{no-firth | firth-fallback | firth}]
7669 ['cols='<col set desc.>] ['local-covar='<file>] ['local-pvar='<file>]
7670 ['local-psam='<file>] ['local-omit-last' | 'local-cats='<category ct>]
7671 Basic association analysis on quantitative and/or case/control phenotypes.
7672 For each variant, a linear (for quantitative traits) or logistic (for
7673 case/control) regression is run with the phenotype as the dependent
7674 variable, and nonmajor allele dosage(s) and a constant-1 column as
7675 predictors.
7676 * There is usually an additive effect line for every nonmajor allele, and
7677 no such line for the major allele. To omit REF alleles instead of major
7678 alleles, add the 'omit-ref' modifier. (When performing interaction
7679 testing, this tends to cause the multicollinearity check to fail for
7680 low-ref-frequency variants.)
7681 * By default, sex (male = 1, female = 2; note that this is a change from
7682 PLINK 1.x) is automatically added as a predictor for X chromosome
7683 variants, and no others. The 'sex' modifier causes it to be added
7684 everywhere (except chrY), while 'no-x-sex' excludes it entirely.
7685 * The 'log10' modifier causes p-values to be reported in -log10(p) form.
7686 * 'pheno-ids' causes the samples used in each set of regressions to be
7687 written to an .id file. (When the samples differ on chrX or chrY, .x.id
7688 and/or .y.id files are also written.)
7689 * The 'genotypic' modifier adds an additive effect/dominance deviation 2df
7690 joint test (0-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and
7691 0..1..0 coding instead.
7692 * 'dominant' and 'recessive' specify a model assuming full dominance or
7693 recessiveness, respectively, for the ref allele. I.e. the genotype
7694 column is recoded as 0..1..1 or 0..0..1, respectively.
7695 * 'interaction' adds genotype x covariate interactions to the model. Note
7696 that this tends to produce 'NA' results (due to the multicollinearity
7697 check) when the reference allele is 'wrong'; --maj-ref can be used to
7698 enable analysis of those variants.
7699 * Additional predictors can be added with --covar. By default, association
7700 statistics are reported for all nonconstant predictors; 'hide-covar'
7701 suppresses covariate-only results, while 'intercept' causes intercepts
7702 to be reported.
7703 * For logistic regression, when the phenotype [quasi-]separates the
7704 genotype, an NA result is currently reported by default. To fall back on
7705 Firth logistic regression instead when the basic logistic regression
7706 fails to converge, add the 'firth-fallback' modifier (highly recommended,
7707 will become the default when beta testing begins). To eliminate the
7708 special case and use Firth logistic regression everywhere, add 'firth'.
7709 'no-firth' can be used to prevent Firth regression from being attempted
7710 in a way that'll still work after alpha testing completes.
7711 * To add covariates which are not constant across all variants, add the
7712 'local-covar=', 'local-pvar=', and 'local-psam=' modifiers, and use full
7713 filenames for each.
7714 Normally, the local-covar file should have c * n real-valued columns,
7715 where the first c columns correspond to the first sample in the
7716 local-psam file, columns (c+1) to 2c correspond to the second sample,
7717 etc.; and the mth line corresponds to the mth nonheader line of the
7718 local-pvar file. (Variants outside of the local-pvar file are excluded
7719 from the regression.) The local covariates are assigned the names
7720 LOCAL1, LOCAL2, etc.; to exclude the last local covariate from the
7721 regression (necessary if they are e.g. local ancestry coefficients which
7722 sum to 1), add 'local-omit-last'.
7723 Alternatively, with 'local-cats='<k>, the local-covar file is expected to
7724 have n columns with integer-valued entries in [1, k]. These category
7725 assignments are expanded into (k-1) local covariates in the usual manner.
7726 The main report supports the following column sets:
7727 chrom: Chromosome ID.
7728 pos: Base-pair coordinate.
7729 (ID is always present, and positioned here.)
7730 ref: Reference allele.
7731 alt1: Alternate allele 1.
7732 alt: All alternate alleles, comma-separated.
7733 (A1 is always present, and positioned here. For multiallelic variants,
7734 this column may contain multiple comma-separated alleles when the result
7735 doesn't depend on which allele is A1.)
7736 ax: Non-A1 alleles, comma-separated.
7737 a1count: A1 allele count (can be decimal with dosage data).
7738 totallele: Allele observation count (can be higher than --freq value, due
7739 to inclusion of het haploids and chrX model).
7740 a1countcc: A1 count in cases, then controls (case/control only).
7741 totallelecc: Case and control allele observation counts.
7742 gcountcc: Genotype hardcall counts (neither-A1, het-A1, A1-A1) in cases,
7743 then controls (case/control only).
7744 a1freq: A1 allele frequency.
7745 a1freqcc: A1 frequency in cases, then controls (case/control only).
7746 machr2: Unphased MaCH imputation quality (frequently labeled 'INFO').
7747 firth: Reports whether Firth regression was used (firth-fallback only).
7748 test: Test identifier. (Required unless only one test is run.)
7749 nobs: Number of samples in the regression.
7750 beta: Regression coefficient (for A1 if additive test).
7751 orbeta: Odds ratio for case/control, beta for quantitative traits.
7752 (Ignored if 'beta' column set included.)
7753 se: Standard error of beta.
7754 ci: Bounds of symmetric approximate confidence interval (requires --ci).
7755 tz: T-statistic for linear regression, Wald Z-score for logistic/Firth.
7756 p: Asymptotic p-value (or -log10(p)) for T/Z-statistic.
7757 err: Error code for NA results.
7758 The default is chrom,pos,ref,alt,firth,test,nobs,orbeta,se,ci,tz,p.
7759
7760 --score <filename> [i] [j] [k] [{header | header-read}]
7761 [{center | variance-standardize | dominant | recessive}]
7762 ['no-mean-imputation'] ['se'] ['zs'] ['ignore-dup-ids']
7763 [{list-variants | list-variants-zs}] ['cols='<col set descriptor>]
7764 Apply linear scoring system(s) to each sample.
7765 The input file should have one line per scored variant. Variant IDs are
7766 read from column #i and allele codes are read from column #j, where i
7767 defaults to 1 and j defaults to i+1. For now, only one allele per
7768 multiallelic variant may be assigned an explicit score; contact us if you
7769 need this changed.
7770 * By default, a single column of input coefficients is read from column #k,
7771 where k defaults to j+1. (--score-col-nums can be used to specify
7772 multiple columns.)
7773 * 'header-read' causes the first line of the input file to be treated as a
7774 header line containing score names. Otherwise, score(s) are assigned the
7775 names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line
7776 to be entirely ignored.
7777 * By default, copies of unnamed alleles contribute zero to score, while
7778 missing genotypes contribute an amount proportional to the loaded (via
7779 --read-freq) or imputed allele frequency. To throw out missing
7780 observations instead (decreasing the denominator in the final average
7781 when this happens), use the 'no-mean-imputation' modifier.
7782 * You can use the 'center' modifier to shift all genotypes to mean zero, or
7783 'variance-standardize' to linearly transform the genotypes to mean-0,
7784 variance-1.
7785 * The 'dominant' modifier causes dosages greater than 1 to be treated as 1,
7786 while 'recessive' uses max(dosage - 1, 0) on diploid chromosomes.
7787 ('dominant', 'recessive', and 'variance-standardize' cannot be used with
7788 chrX.)
7789 * The 'se' modifier causes the input coefficients to be treated as
7790 independent standard errors; in this case, standard errors for the score
7791 average/sum are reported. (Note that this will systematically
7792 underestimate standard errors when scored variants are in LD.)
7793 * By default, --score errors out if a variant ID in the input file appears
7794 multiple times in the main dataset. Use the 'ignore-dup-ids' modifier to
7795 skip them instead (a warning is still printed if such variants are
7796 present).
7797 * The 'list-variants[-zs]' modifier causes variant IDs used for scoring to
7798 be written to <output prefix>.sscore.vars[.zst].
7799 The main report supports the following column sets:
7800 maybefid: FID, if that column was in the input.
7801 fid: Force FID column to be written even when absent in the input.
7802 (IID is always present, and positioned here.)
7803 maybesid: SID, if that column was in the input.
7804 sid: Force SID column to be written even when absent in the input.
7805 pheno1: First active phenotype.
7806 phenos: All active phenotypes, if any.
7807 nmissallele: Number of nonmissing alleles.
7808 denom: Denominator of score average (equal to nmissallele value when
7809 'no-mean-imputation' specified).
7810 dosagesum: Sum of named allele dosages.
7811 scoreavgs: Score averages.
7812 scoresums: Score sums.
7813 The default is maybefid,maybesid,phenos,nmissallele,dosagesum,scoreavgs.
7814 For more sophisticated polygenic risk scoring, we recommend the PRSice-2
7815 software package (https://www.prsice.info/ ).
7816
7817 --variant-score <filename> ['zs'] ['bin' | 'cols='<col set descriptor>]
7818 (alias: --vscore)
7819 Apply linear scoring system(s) to each variant. Each reported variant
7820 score is the dot product of a sample-weight vector with the
7821 total-ALT-dosage vector, with MAF-based mean imputation applied to missing
7822 dosages.
7823 Input file format: one line per sample, each starting with an ID and
7824 followed by scoring weight(s); it can also have a header line with the
7825 sample ID representation and the score name(s).
7826 The usual .vscore text report supports the following column sets:
7827 chrom: Chromosome ID.
7828 pos: Base-pair coordinate.
7829 (ID is always present, and positioned here.)
7830 ref: Reference allele.
7831 alt1: Alternate allele 1.
7832 alt: All alternate alleles, comma-separated.
7833 altfreq: ALT allele frequency used for mean-imputation.
7834 nmiss: Number of missing (and thus mean-imputed) dosages.
7835 nobs: Number of (nonmissing) sample observations.
7836 (Variant scores are always present, and positioned here.)
7837 Default is chrom,pos,ref,alt.
7838 If binary output is requested instead, the main .vscore.bin matrix contains
7839 double-precision floating-point values, column (score) ID(s) are saved to a
7840 <output prefix>.vscore.cols, and variant IDs are saved to
7841 <output prefix>.vscore.vars[.zst].
7842
7843 --adjust-file <filename> ['zs'] ['gc'] ['cols='<column set descriptor>]
7844 ['log10'] ['input-log10'] ['test='<test name, case-sensitive>]
7845 Given a file with unfiltered association test results, report some basic
7846 multiple-testing corrections, sorted in increasing-p-value order.
7847 * 'gc' causes genomic-controlled p-values to be used in the formulas.
7848 (This tends to be overly conservative. We note that LD Score regression
7849 usually does a better job of calibrating lambda; see Lee JJ, McGue M,
7850 Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an
7851 estimator of confounding and genetic correlations in genome-wide
7852 association studies.)
7853 * 'log10' causes negative base 10 logs of p-values to be reported, instead
7854 of raw p-values. 'input-log10' specifies that the input file contains
7855 -log10(p) values.
7856 * If the input file contains multiple tests per variant which are
7857 distinguished by a 'TEST' column (true for --linear/--logistic/--glm),
7858 you must use 'test=' to select the test to process.
7859 The following column sets are supported:
7860 chrom: Chromosome ID.
7861 pos: Base-pair coordinate.
7862 (ID is always present, and positioned here.)
7863 ref: Reference allele.
7864 alt1: Alternate allele 1.
7865 alt: All alternate alleles, comma-separated.
7866 a1: Tested allele. (Omitted if missing from input file.)
7867 unadj: Unadjusted p-value.
7868 gc: Devlin & Roeder (1999) genomic control corrected p-value (additive
7869 models only).
7870 qq: P-value quantile.
7871 bonf: Bonferroni correction.
7872 holm: Holm-Bonferroni (1979) adjusted p-value.
7873 sidakss: Sidak single-step adjusted p-value.
7874 sidaksd: Sidak step-down adjusted p-value.
7875 fdrbh: Benjamini & Hochberg (1995) step-up false discovery control.
7876 fdrby: Benjamini & Yekutieli (2001) step-up false discovery control.
7877 Default set is chrom,a1,unadj,gc,bonf,holm,sidakss,sidaksd,fdrbh,fdrby.
7878 --genotyping-rate ['dosage']
7879 Report genotyping rate in log (this was automatic in PLINK 1.x).
7880
7881 --pgen-info
7882 Reports basic information about a .pgen file.
7883
7884 --validate
7885 Validates all variant records in a .pgen file.
7886
7887 --zst-decompress <.zst file> [output filename]
7888 (alias: --zd)
7889 Decompress a Zstd-compressed file. If no output filename is specified, the
7890 file is decompressed to standard output.
7891 This cannot be used with any other flags, and does not cause a log file to
7892 be generated.
7893
7894 The following other flags are supported.
7895 --script <fname> : Include command-line options from file.
7896 --rerun [log] : Rerun commands in log (default 'plink2.log').
7897 --version : Display only version number before exiting.
7898 --silent : Suppress regular output to console. (Error-output is
7899 not suppressed.)
7900 --double-id : Set both FIDs and IIDs to the VCF/.bgen sample ID.
7901 --const-fid [ID] : Set all FIDs to the given constant. If '0' (the
7902 default), no FID column is created.
7903 --id-delim [d] : Normally parses single-delimiter sample IDs as
7904 <FID><d><IID>, and double-delimiter IDs as
7905 <FID><d><IID><d><SID>; default delimiter is '_'.
7906 --id-delim can no longer be used with
7907 --double-id/--const-fid; it will error out if any ID
7908 lacks the delimiter.
7909 --idspace-to <c> : Convert spaces in VCF/.bgen sample IDs to the given
7910 character.
7911 --iid-sid : Make --id-delim and --sample-diff interpret two-token
7912 sample IDs as IID-SID instead of FID-IID.
7913 --vcf-require-gt : Skip variants with no GT field.
7914 --vcf-min-gq <val> : No-call genotypes when GQ is present and below the
7915 threshold.
7916 --vcf-max-dp <val> : No-call genotypes when DP is present and above/below
7917 --vcf-min-dp <val> the threshold.
7918 --vcf-half-call <m> : Specify how '0/.' and similar VCF GT values should be
7919 handled. The following four modes are supported:
7920 * 'error'/'e' (default) errors out and reports line #.
7921 * 'haploid'/'h' treats them as haploid calls.
7922 * 'missing'/'m' treats them as missing.
7923 * 'reference'/'r' treats the missing value as 0.
7924 --oxford-single-chr <chr name> : Specify single-chromosome .gen/.bgen file
7925 with no useful chromosome info inside.
7926 --missing-code [string list] : Comma-delimited list of missing phenotype
7927 (alias: --missing_code) values for Oxford-format import (default
7928 'NA').
7929 --hard-call-threshold <val> : When importing dosage data, a hardcall is
7930 normally saved when the distance from the
7931 nearest hardcall, defined as
7932 0.5 * sum_i |x_i - round(x_i)|
7933 (where the x_i's are 0..2 allele dosages),
7934 is not greater than 0.1. You can adjust
7935 this threshold by providing a numeric
7936 parameter to --hard-call-threshold.
7937 You can also use this with --make-[b]pgen
7938 to alter the saved hardcalls while leaving
7939 the dosages untouched, or --make-bed to
7940 tweak hardcall export.
7941 --dosage-erase-threshold <val> : --hard-call-threshold normally preserves
7942 the original dosages, and several PLINK 2
7943 commands use them when they're available.
7944 Use --dosage-erase-threshold to make PLINK
7945 2 erase dosages and keep only hardcalls
7946 when distance-from-hardcall <= the given
7947 level.
7948 --import-dosage-certainty <val> : The PLINK 2 file format currently supports
7949 a single dosage for each allele. Some
7950 other dosage file formats include a
7951 separate probability for every possible
7952 genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52,
7953 P(1/1)=0.28}, a highly uncertain call that
7954 is nevertheless treated as a hardcall under
7955 '--hard-call-threshold 0.1'. To make PLINK
7956 2 treat a dosage as missing whenever the
7957 largest probability is less than a
7958 threshold, use --import-dosage-certainty.
7959 --input-missing-genotype <c> : '.' is always interpreted as a missing
7960 genotype code in input files. By default, '0'
7961 also is; you can change this second missing
7962 code with --input-missing-genotype.
7963 --allow-extra-chr : Permit unrecognized chromosome codes (alias --aec).
7964 --chr-set <autosome ct> ['no-x'] ['no-y'] ['no-xy'] ['no-mt'] :
7965 Specify a nonhuman chromosome set. The first parameter sets the number of
7966 diploid autosome pairs if positive, or haploid chromosomes if negative.
7967 Given diploid autosomes, the remaining modifiers indicate the absence of
7968 the named non-autosomal chromosomes.
7969 --cow/--dog/--horse/--mouse/--rice/--sheep : Shortcuts for those species.
7970 --autosome-num <val> : Alias for '--chr-set <value> no-y no-xy no-mt'.
7971 --human : Explicitly specify human chromosome set, and make
7972 output .pvar/VCF files include a ##chrSet header
7973 line. (.pvar/VCF output files automatically
7974 include ##chrSet when a nonhuman set is specified.)
7975 --chr-override ['file'] : By default, if --chr-set/--autosome-num/--cow/etc.
7976 conflicts with an input file ##chrSet header line,
7977 PLINK 2 will error out. --chr-override with no
7978 parameter causes the command line to take
7979 precedence; '--chr-override file' defers to the
7980 file.
7981 --var-min-qual <val> : Skip variants with low/missing QUAL.
7982 --var-filter [exception(s)...] : Skip variants which have FILTER failures.
7983 --extract-if-info <key> <op> <val> : Exclude variants which don't/do satisfy
7984 --exclude-if-info <key> <op> <val> a comparison predicate on an INFO key,
7985 (aliases: --extract-if, e.g.
7986 --exclude-if) --extract-if-info "VT == SNP"
7987 Unless the operator is !=, the predicate
7988 always evaluates to false when the key
7989 is missing.
7990 --require-info <key(s)...> : Exclude variants based on nonexistence
7991 --require-no-info <key(s)...> or existence of an INFO key. "<key>=."
7992 is treated as nonexistence.
7993 --extract-col-cond <f> [valcol] [IDcol] [skip] :
7994 --extract-col-cond-match <(sub)string(s)...>
7995 --extract-col-cond-mismatch <(sub)string(s)...>
7996 --extract-col-cond-substr
7997 --extract-col-cond-min <min>
7998 --extract-col-cond-max <max> :
7999 Exclude all variants without a value-column entry satisfying a condition.
8000 * By default, values are read from column 2 of the file, and variant IDs
8001 are read from column 1.
8002 * Three types of conditions are supported:
8003 * When --extract-col-cond-match is specified without
8004 --extract-col-cond-substr, the value is checked for equality with the
8005 given strings, and kept iff one of them matches. Similarly,
8006 --extract-col-cond-mismatch without --extract-col-cond-substr causes
8007 the variant to be kept iff the value matches none of the given strings.
8008 * When --extract-col-cond-match and/or -mismatch are specified with
8009 --extract-col-cond-substr, the variant is kept iff none of the
8010 --extract-col-cond-mismatch substrings are contained in the value, and
8011 either --extract-col-cond-match was unspecified or at least one of its
8012 substrings is contained.
8013 * Otherwise, the value is interpreted as a number, and the variant is
8014 kept if the number is in [<min>, <max>] (default min=0, max=DBL_MAX).
8015 --pheno ['iid-only'] <f> : Specify additional phenotype/covariate file.
8016 Comma-delimited files with a header line are now
8017 permitted.
8018 --pheno-name <name...> : Only load the designated phenotype(s) from the
8019 --pheno (if one was specified) or .psam (if no
8020 --pheno) file. Separate multiple names with
8021 spaces or commas, and use dashes to designate
8022 ranges.
8023 --pheno-col-nums <#...> : Only load the phenotype(s) in the designated
8024 column number(s) from the --pheno file.
8025 --no-psam-pheno : Ignore phenotype(s) in .psam/.fam file.
8026 --strict-sid0 : By default, if there is no SID column in the .psam/.fam
8027 (or --update-ids) file, but there is one in another
8028 input file (for e.g. --keep/--remove), the latter SID
8029 column is ignored; sample IDs are considered matching as
8030 long as FID and IID are equal (with missing FID treated
8031 as '0'). If you also want to require SID = '0' for a
8032 sample ID match in this situation, add --strict-sid0.
8033 --input-missing-phenotype <v> : Set nonzero number to treat as a missing
8034 pheno/covar in input files (default -9).
8035 --no-input-missing-phenotype : Don't treat any nonzero number as a missing
8036 pheno/covar. ('NA'/'nan' are still treated
8037 as missing.)
8038 --1 : Expect case/control phenotypes in input files
8039 to be coded as 0 = control, 1 = case, instead
8040 of the usual 0 = missing, 1 = ctrl, 2 = case.
8041 (Unlike PLINK 1.x, this does not force all
8042 phenotypes to be interpreted as case/ctrl.)
8043 --missing-catname <str> : Set missing-categorical-phenotype string
8044 (case-sensitive, default 'NONE').
8045 --covar ['iid-only'] <f> : Specify additional covariate file.
8046 Comma-delimited files with a header line are now
8047 permitted.
8048 --covar-name <name...> : Only load the designated covariate(s) from the
8049 --covar (if one was specified), --pheno (if no
8050 --covar), or .psam (if no --covar or --pheno)
8051 file.
8052 --covar-col-nums <#...> : Only load the covariate(s) in the designated
8053 column number(s) from the --covar (if one was
8054 specified) or --pheno (if no --covar) file.
8055 --within <f> [new pheno name] : Import a PLINK 1.x categorical phenotype.
8056 (Phenotype name defaults to 'CATPHENO'.)
8057 * If any numeric values are present, ALL
8058 values must be numeric. In that case, 'C'
8059 is added in front of all category names.
8060 * 'NA' is treated as a missing value.
8061 --mwithin <n> : Load --within categories from column n+2.
8062 --family [new pheno name] : Create a categorical phenotype from FID.
8063 Restrictions on and handling of numeric
8064 values are the same as for --within.
8065 --family-missing-catname <nm> : Make --family treat the specified FID as
8066 missing.
8067 --keep <fname...> : Exclude all samples not named in a file.
8068 --remove <fname...> : Exclude all samples named in a file.
8069 --keep-fam <fn...> : Exclude all families not named in a file.
8070 --remove-fam <f...> : Exclude all families named in a file.
8071 --extract [{bed0 | bed1}] <f...> : Usually excludes all variants (not) named
8072 --exclude [{bed0 | bed1}] <f...> in the given file(s). When multiple files
8073 are named, they are concatenated.
8074 With the 'bed0' or 'bed1' modifier,
8075 variants outside/inside the positional
8076 ranges in the interval-BED file(s) are
8077 excluded instead. 'bed0' tells PLINK 2 to
8078 assume the interval bounds follow the UCSC
8079 0-based half-open convention, while 'bed1'
8080 (equivalent to PLINK 1.9 'range')
8081 specifies 1-based fully-closed.
8082 --extract-intersect [{bed0 | bed1}] <f...> : Just like --extract, except that
8083 a variant must be in the
8084 intersection, rather than just
8085 the union, of the files to
8086 remain.
8087 --keep-cats <filename> : These can be used individually or in combination
8088 --keep-cat-names <nm...> to define a list of categories to keep; all
8089 samples not in one of the named categories are
8090 excluded. Use spaces to separate category names
8091 for --keep-cat-names. Use the --missing-catname
8092 value (default 'NONE') to refer to the group of
8093 uncategorized samples.
8094 --keep-cat-pheno <pheno> : If more than one categorical phenotype is loaded,
8095 or you wish to filter on a categorical covariate,
8096 --keep-cat-pheno must be used to specify which
8097 phenotype/covariate --keep-cats and
8098 --keep-cat-names apply to.
8099 --remove-cats <filename> : Exclude all categories named in the file.
8100 --remove-cat-names <...> : Exclude named categories.
8101 --remove-cat-pheno <phe> : Specify pheno for --remove-cats/remove-cat-names.
8102 --split-cat-pheno [{omit-most | omit-last}] ['covar-01']
8103 [cat. pheno/covar name(s)...] :
8104 Split n-category phenotype(s) into n (or n-1, with 'omit-most'/'omit-last')
8105 binary phenotypes, with names of the form <orig. pheno name>=<cat. name>.
8106 (As a consequence, affected phenotypes and categories are not permitted to
8107 contain the '=' character.)
8108 * This happens after all sample filters.
8109 * If no phenotype or covariate names are provided, all categorical
8110 phenotypes (but not covariates) are processed.
8111 * By default, generated covariates are coded as 1=false, 2=true. To code
8112 them as 0=false, 1=true instead, add the 'covar-01' modifier.
8113 --loop-cats <pheno/covar> : Run variant filters and subsequent operations
8114 on just the samples in the first category; then
8115 just the samples in the second category; and so
8116 on, for all categories in the named categorical
8117 phenotype.
8118 --no-id-header ['iid-only'] : Don't include a header line in .id output
8119 files. This normally forces two-column FID/IID
8120 output; add 'iid-only' to force just
8121 single-column IID.
8122 --variance-standardize [pheno/covar name(s)...]
8123 --covar-variance-standardize [covar name(s)...] :
8124 Linearly transform named covariates (and quantitative phenotypes, if
8125 --variance-standardize) to mean-zero, variance 1. If no parameters are
8126 provided, all possible phenotypes/covariates are affected.
8127 This is frequently necessary to prevent multicollinearity when dealing with
8128 covariates where abs(mean) is much larger than abs(standard deviation),
8129 such as year of birth.
8130 --quantile-normalize [...] : Force named covariates and quantitative
8131 --pheno-quantile-normalize [...] phenotypes to a N(0,1) distribution,
8132 --covar-quantile-normalize [...] preserving only the original rank orders.
8133 --chr <chr(s)...> : Exclude all variants not on the given chromosome(s).
8134 Valid choices for humans are 0 (unplaced), 1-22, X, Y,
8135 XY, MT, PAR1, and PAR2. Separate multiple chromosomes
8136 with spaces and/or commas, and use a dash (no adjacent
8137 spaces permitted) to denote a range, e.g.
8138 '--chr 1-4, 22, par1, x, par2'.
8139 --not-chr <...> : Reverse of --chr (exclude variants on listed
8140 chromosomes).
8141 --autosome : Exclude all non-autosomal variants.
8142 --autosome-par : Exclude all non-autosomal variants, except those in a
8143 pseudo-autosomal region.
8144 --snps-only ['just-acgt'] : Exclude non-SNP variants. By default, SNP = all
8145 allele codes are single-character (so
8146 multiallelic variants with a mix of SNPs and
8147 non-SNPs are excluded; split your variants first
8148 if that's a problem).
8149 The 'just-acgt' modifier restricts SNP codes to
8150 {A,C,G,T,a,c,g,t,<missing>}.
8151 --from <var ID> : Use ID(s) to specify a variant range to load. When used
8152 --to <var ID> together, both variants must be on the same chromosome.
8153 (--snps can be used to specify intervals which cross
8154 chromosome boundaries.)
8155 --snp <var ID> : Specify a single variant to load.
8156 --exclude-snp <ID> : Specify a single variant to exclude.
8157 --window <kbs> : With --snp/--exclude-snp, loads/excludes all variants
8158 within half the specified kb distance of the named one.
8159 --from-bp <pos> : Use base-pair coordinates to define a variant range to
8160 --to-bp <pos> load.
8161 --from-kb <pos> * You must use these with --chr, specifying a single
8162 --to-kb <pos> chromosome.
8163 --from-mb <pos> * Decimals and negative numbers are permitted.
8164 --to-mb <pos> * The --to-bp(/-kb/-mb) position is no longer permitted
8165 to be smaller than the --from-bp position.
8166 --snps <var IDs...> : Use IDs to specify variant range(s) to load or
8167 --exclude-snps <...> exclude. E.g. '--snps rs1111-rs2222, rs3333, rs4444'.
8168 --force-intersect : PLINK 2 normally errors out when multiple variant
8169 inclusion filters (--extract, --extract-col-cond,
8170 --extract-intersect, --from/--to, --from-bp/--to-bp,
8171 --snp, --snps) are specified. --force-intersect
8172 allows the run to proceed; the set intersection will
8173 be taken.
8174 --thin <p> : Randomly remove variants, retaining each with prob. p.
8175 --thin-count <n> : Randomly remove variants until n of them remain.
8176 --bp-space <bps> : Remove variants so that each pair is no closer than
8177 the given bp distance.
8178 --thin-indiv <p> : Randomly remove samples, retaining with prob. p.
8179 --thin-indiv-count <n> : Randomly remove samples until n of them remain.
8180 --keep-col-match <f> <val(s)...> : Exclude all samples without a 3rd column
8181 entry in the given file exactly matching
8182 one of the given strings. (Separate
8183 multiple strings with spaces.)
8184 --keep-col-match-name <col name> : Check column with given name instead.
8185 --keep-col-match-num <n> : Check nth column instead.
8186 --geno [val] [{dosage | hh-missing}]
8187 --mind [val] [{dosage | hh-missing}] :
8188 Exclude variants (--geno) and/or samples (--mind) with missing call
8189 frequencies greater than a threshold (default 0.1). (Note that the default
8190 threshold is only applied if --geno/--mind is invoked without a parameter;
8191 when --geno/--mind is not invoked, no missing call frequency ceiling is
8192 enforced at all. Other inclusion/exclusion default thresholds work the
8193 same way.)
8194 By default, when a dosage is present but a hardcall is not, the genotype is
8195 treated as missing; add the 'dosage' modifier to treat this case as
8196 nonmissing. Alternatively, you can use 'hh-missing' to also treat
8197 heterozygous haploid calls as missing.
8198 --require-pheno [name(s)...] : Remove samples missing any of the named
8199 --require-covar [name(s)...] phenotype(s)/covariate(s). If no parameters
8200 are provided, all phenotype(s)/covariate(s)
8201 must be present.
8202 --maf [freq] [mode] : Exclude variants with allele frequency lower than a
8203 (alias: --min-af) threshold (default 0.01). By default, the nonmajor
8204 allele frequency is used; the other supported modes
8205 are 'nref' (non-reference), 'alt1', and 'minor'
8206 (least frequent). bcftools freq:mode notation is
8207 permitted.
8208 --max-maf <freq> [mode] : Exclude variants with MAF greater than the
8209 (alias: --max-af) threshold.
8210 --mac <ct> [mode] : Exclude variants with allele dosage lower than the
8211 (alias: --min-ac) given threshold.
8212 --max-mac <ct> [mode] : Exclude variants with allele dosage greater than
8213 (alias: --max-ac) the given threshold.
8214 --maf-succ : Rule of succession allele frequency estimation (used in
8215 EIGENSOFT). Given j observations of one allele and k
8216 observations of the other for a biallelic variant, infer
8217 allele frequencies of (j+1) / (j+k+2) and
8218 (k+1) / (j+k+2), rather than the default j / (j+k) and
8219 k / (j+k).
8220 Note that this does not affect --freq's output.
8221 --min-alleles <ct> : Exclude variants with fewer than the given # of alleles.
8222 (When a variant has exactly one ALT allele, and it's
8223 a missing-code, it's excluded by "--min-alleles 2".)
8224 --max-alleles <ct> : Exclude variants with more than the given # of alleles.
8225 --read-freq <file> : Load allele frequency estimates from the given --freq or
8226 --geno-counts (or PLINK 1.9 --freqx) report, instead of
8227 imputing them from the immediate dataset.
8228 --hwe <p> ['midp'] ['keep-fewhet'] :
8229 Exclude variants with Hardy-Weinberg equilibrium exact test p-values below
8230 a threshold.
8231 * By default, only founders are considered.
8232 * chrX p-values are now computed using Graffelman and Weir's method.
8233 * For variants with k alleles with k>2, k separate 'biallelic' tests are
8234 performed, and the variant is filtered out if any of them fail.
8235 * With 'keep-fewhet', variants which fail the test in the too-few-hets
8236 direction are not excluded. On chrX, this uses the ratio between the
8237 Graffelman/Weir p-value and the female-only p-value.
8238 * There is currently no special handling of case/control phenotypes.
8239 --mach-r2-filter [min] [max] : Exclude variants with MaCH imputation quality
8240 metric less than min or greater than max
8241 (defaults 0.1 and 2.0). (Monomorphic
8242 variants, with r2 = nan, are not excluded.)
8243 * This is NOT identical to the R2 metric
8244 reported by Minimac3 0.1.13+; see below.
8245 * If a single parameter is provided, it is
8246 treated as the minimum.
8247 * The metric is not computed on chrX and MT.
8248 --minimac3-r2-filter <min> [max] : Compute Minimac3 R2 values from scratch,
8249 and exclude variants with R2 less than min
8250 or (if max is provided) greater than max.
8251 * Note that this requires phased-dosage
8252 data for all samples and variants;
8253 otherwise this will systematically
8254 underestimate imputation quality, since
8255 unphased hardcalls/dosages are treated
8256 as if they were maximally uncertain.
8257 (Use --extract-if-info/--exclude-if-info
8258 to filter on precomputed Minimac3 R2 in
8259 a VCF/.pvar INFO column.)
8260 --keep-females : Exclude male and unknown-sex samples.
8261 --keep-males : Exclude female and unknown-sex samples.
8262 --keep-nosex : Exclude all known-sex samples.
8263 --remove-females : Exclude female samples.
8264 --remove-males : Exclude male samples.
8265 --remove-nosex : Exclude unknown-sex samples.
8266 --keep-founders : Exclude nonfounder samples.
8267 --keep-nonfounders : Exclude founder samples.
8268 --keep-if <pheno/covar> <op> <val> : Exclude samples which don't/do satisfy a
8269 --remove-if <pheno/covar> <op> <v> comparison predicate, e.g.
8270 --keep-if "PHENO1 == case"
8271 Unless the operator is !=, the predicate
8272 always evaluates to false when the
8273 phenotype/covariate is missing.
8274 --nonfounders : Include nonfounders in allele freq/HWE calculations.
8275 --bad-freqs : When PLINK 2 needs decent allele frequencies, it
8276 normally errors out if they aren't provided by
8277 --read-freq and less than 50 founders are available to
8278 impute them from. Use --bad-freqs to force PLINK 2 to
8279 proceed in this case.
8280 --export-allele <file> : With --export A/A-transpose/AD, count alleles named
8281 in the file, instead of REF alleles.
8282 --output-chr <MT code> : Set chromosome coding scheme in output files by
8283 providing the desired human mitochondrial code.
8284 Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM',
8285 and 'chrMT'; default is now 'MT' (note that this is
8286 a change from PLINK 1.x, which defaulted to '26').
8287 --output-missing-genotype <ch> : Set the code used to represent missing
8288 genotypes in output files (default '.').
8289 --output-missing-phenotype <s> : Set the string used to represent missing
8290 phenotypes in output files (default 'NA').
8291 --sort-vars [mode] : Sort variants by chromosome, then position, then
8292 ID. The following string orders are supported:
8293 * 'natural'/'n': Natural sort (default).
8294 * 'ascii'/'a': ASCII.
8295 This must be used with --make-[b]pgen/--make-bed.
8296 --set-hh-missing ['keep-dosage'] : Make --make-[b]pgen/--make-bed set non-MT
8297 heterozygous haploid hardcalls, and all
8298 female chrY calls, to missing. (Unlike
8299 PLINK 1.x, this treats unknown-sex chrY
8300 genotypes like males, not females.)
8301 By default, all associated dosages are
8302 also erased; use 'keep-dosage' to keep
8303 them all.
8304 --set-mixed-mt-missing ['keep-dosage'] : Make --make-[b]pgen/--make-bed set
8305 mixed MT hardcalls to missing.
8306 --split-par <bp1> <bp2> : Changes chromosome code of all X chromosome
8307 --split-par <build> variants with bp position <= bp1 to PAR1, and those
8308 with position >= bp2 to PAR2. The following build
8309 codes are supported as shorthand:
8310 * 'b36'/'hg18' = NCBI 36, 2709521/154584237
8311 * 'b37'/'hg19' = GRCh37, 2699520/154931044
8312 * 'b38'/'hg38' = GRCh38, 2781479/155701383
8313 --merge-par : Merge PAR1/PAR2 back with X. Requires PAR1 to be
8314 positioned immediately before X, and PAR2 to be
8315 immediately after X. (Should *not* be used with
8316 "--export vcf", since it causes male
8317 homozygous/missing calls in PAR1/PAR2 to be
8318 reported as haploid.)
8319 --merge-x : Merge XY back with X. This usually has to be
8320 combined with --sort-vars.
8321 --set-missing-var-ids <t> : Given a template string with a '@' where the
8322 --set-all-var-ids <t> chromosome code should go and '#' where the bp
8323 coordinate belongs, --set-missing-var-ids
8324 assigns chromosome-and-bp-based IDs to unnamed
8325 variants, while --set-all-var-ids resets all
8326 IDs.
8327 You may also use '$r'/'$a' to refer to the
8328 ref and alt1 alleles, or '$1'/'$2' to refer to
8329 them in alphabetical order.
8330 --var-id-multi <t> : Specify alternative templates for multiallelic
8331 --var-id-multi-nonsnp <t> variants. ('$a' and '$1'/'$2' should be avoided
8332 here, though they're technically still allowed.)
8333 --new-id-max-allele-len <len> [{error | missing | truncate}] :
8334 Specify maximum number of leading characters from allele codes to include
8335 in new variant IDs, and behavior on longer codes (defaults 23, error).
8336 --missing-var-code <str> : Change unnamed variant code for --rm-dup,
8337 --set-{missing|all}-var-ids, and
8338 --recover-var-ids (default '.').
8339 --update-map <f> [bpcol] [IDcol] [skip] : Update variant bp positions.
8340 --update-name <f> [newcol] [oldcol] [skip] : Update variant IDs.
8341 --recover-var-ids <file> ['strict-bim-order'] [{rigid | force}] ['partial'] :
8342 Undo --set-all-var-ids, given the original .pvar/VCF/.bim file. Original
8343 IDs are looked up by position and allele codes.
8344 * By default, if the original-ID file is a .bim, allele order is ignored.
8345 Use 'strict-bim-order' to force A1=ALT, A2=REF.
8346 * If any variant has multiple matching records in the original-ID file, and
8347 the IDs conflict, --recover-var-ids writes the affected (current) ID(s)
8348 to <output prefix>.recoverid.dup, and normally errors out. If the
8349 original-ID file has the same number of variants in the same order, you
8350 can still recover the old IDs with the 'rigid' modifier in this case.
8351 Alternatively, to proceed and assign the missing-ID code to these
8352 variants, add the 'force' modifier. (The .recoverid.dup file is still
8353 written when 'rigid' or 'force' is specified.)
8354 * --recover-var-ids normally expects to replace all variant IDs, and errors
8355 out if any are left untouched. Add the 'partial' modifier when you
8356 actually want to update just a proper subset.
8357 --update-alleles <fname> : Update variant allele codes.
8358 --update-ids <fname> : Update sample IDs.
8359 --update-parents <fname> : Update parental IDs.
8360 --update-sex <filename> ['col-num='<n>] ['male0'] :
8361 Update sex information.
8362 * By default, if there is a header line starting with '#FID'/'#IID', sex is
8363 loaded from the first column titled 'SEX' (any capitalization);
8364 otherwise, column 3 is assumed. Use 'col-num=' to force a column number.
8365 * Only the first character in the sex column is processed. By default,
8366 '1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female,
8367 and '0'/'N' is interpreted as unknown-sex. To change this to '0'/'M'/'m'
8368 = male, '1'/'F'/'f' = female, anything else other than '2' = unknown-sex,
8369 add 'male0'.
8370 --real-ref-alleles : Treat A2 alleles in a PLINK 1.x fileset as actual REF
8371 alleles; otherwise they're marked as provisional.
8372 --maj-ref ['force'] : Set major alleles to reference, like PLINK 1.x
8373 automatically did. (Note that this is now opt-in
8374 rather than opt-out; --keep-allele-order is no longer
8375 necessary to prevent allele-swapping.)
8376 * This can only be used in runs with
8377 --make-bed/--make-[b]pgen/--export and no other
8378 commands.
8379 * By default, this only affects variants marked as
8380 having 'provisional' reference alleles. Add 'force'
8381 to apply this to all variants.
8382 * All new reference alleles are marked as provisional.
8383 --ref-allele ['force'] <filename> [refcol] [IDcol] [skip]
8384 --alt1-allele ['force'] <filename> [alt1col] [IDcol] [skip] :
8385 These set the alleles specified in the file to ref (--ref-allele) or alt1
8386 (--alt1-allele). They can be combined in the same run.
8387 * These can only be used in runs with --make-bed/--make-[b]pgen/--export
8388 and no other commands.
8389 * "--ref-allele <VCF filename> 4 3 '#'", which scrapes reference allele
8390 assignments from a VCF file, is especially useful.
8391 * By default, these error out when asked to change a 'known' reference
8392 allele. Add 'force' to permit that (when e.g. switching to a new
8393 reference genome).
8394 * When --alt1-allele changes the previous ref allele to alt1, the previous
8395 alt1 allele is set to reference and marked as provisional.
8396 --ref-from-fa ['force'] : This sets reference alleles from the --fa file when
8397 it can be done unambiguously (note that it's never
8398 possible for deletions or some insertions).
8399 By default, it errors out when asked to change a
8400 'known' reference allele; add the 'force' modifier
8401 to permit that.
8402 --normalize ['list'] : Left-normalize all variants, using the --fa file.
8403 (alias: --norm) (Assumes no differences in capitalization.) The
8404 'list' modifier causes a list of affected variant
8405 IDs to be written to <output prefix>.normalized.
8406 --indiv-sort <mode> [f] : Specify sample ID sort order for merge and
8407 --make-[b]pgen/--make-bed. The following four
8408 modes are supported:
8409 * 'none'/'0' keeps samples in the order they were
8410 loaded. Default for non-merge.
8411 * 'natural'/'n' invokes "natural sort", e.g.
8412 'id2' < 'ID3' < 'id10'. Default when merging.
8413 * 'ascii'/'a' sorts in ASCII order, e.g.
8414 'ID3' < 'id10' < 'id2'.
8415 * 'file'/'f' uses the order in the given file
8416 (named in the last parameter).
8417 --king-table-filter <min> : Specify minimum kinship coefficient for
8418 inclusion in --make-king-table report.
8419 --king-table-subset <f> [kmin] : Restrict current --make-king-table run to
8420 sample pairs listed in the given .kin0 file.
8421 If a second parameter is provided, only
8422 sample pairs with kinship >= that threshold
8423 (in the input .kin0) are processed.
8424 --condition <variant ID> [{dominant | recessive}] ['multiallelic']
8425 --condition-list <fname> [{dominant | recessive}] ['multiallelic'] :
8426 Add the given variant, or all variants in the given file, as --glm
8427 covariates.
8428 By default, this errors out if any of the variants are multiallelic; add
8429 the 'multiallelic' ('m' for short) modifier to allow them. They'll
8430 effectively be split against the major allele (unless --glm's 'omit-ref'
8431 modifier was specified), and all induced covariate names--even for
8432 biallelic variants--will have an underscore followed by the allele code at
8433 the end.
8434 --parameters <...> : Include only the given covariates/interactions in the
8435 --glm model, identified by a list of 1-based indices
8436 and/or ranges of them.
8437 --tests <...> : Perform a (joint) test on the specified term(s) in the
8438 --tests all --glm model, identified by 1-based indices and/or ranges
8439 of them.
8440 * Note that, when --parameters is also present, the
8441 indices refer to the terms remaining AFTER pruning by
8442 --parameters.
8443 * You can use '--tests all' to include all terms.
8444 --vif <max VIF> : Set VIF threshold for --glm multicollinearity check
8445 (default 50). (This is no longer skipped for
8446 case/control phenotypes.)
8447 --max-corr <val> : Skip --glm regression when the absolute value of the
8448 correlation between two predictors exceeds this value
8449 (default 0.999).
8450 --xchr-model <m> : Set the chrX --glm/--condition[-list]/--[v]score model.
8451 * '0' = skip chrX.
8452 * '1' = add sex as a covar on chrX, code males 0..1.
8453 * '2' (default) = chrX sex covar, code males 0..2.
8454 (Use the --glm 'interaction' modifier to test for
8455 interaction between genotype and sex.)
8456 --adjust ['zs'] ['gc'] ['log10'] ['cols='<column set descriptor>] :
8457 For each association test in this run, report some basic multiple-testing
8458 corrections, sorted in increasing-p-value order. Modifiers work the same
8459 way as they do on --adjust-file.
8460 --lambda : Set genomic control lambda for --adjust[-file].
8461 --adjust-chr-field <n...> : Set --adjust-file input field names. When
8462 --adjust-pos-field <n...> multiple parameters are given to these flags,
8463 --adjust-id-field <n...> earlier names take precedence over later ones.
8464 --adjust-ref-field <n...>
8465 --adjust-alt-field <n...>
8466 --adjust-a1-field <n...>
8467 --adjust-test-field <n...>
8468 --adjust-p-field <n...>
8469 --ci <size> : Report confidence ratios for odds ratios/betas.
8470 --pfilter <val> : Filter out assoc. test results with higher p-values.
8471 --score-col-nums <...> : Process all the specified coefficient columns in the
8472 --score file, identified by 1-based indexes and/or
8473 ranges of them.
8474 --q-score-range <range file> <data file> [i] [j] ['header'] ['min'] :
8475 Apply --score to subset(s) of variants in the primary score list(s) based
8476 on e.g. p-value ranges.
8477 * The first file should have range labels in the first column, p-value
8478 lower bounds in the second column, and upper bounds in the third column.
8479 Lines with too few entries, or nonnumeric values in the second or third
8480 column, are ignored.
8481 * The second file should contain a variant ID and a p-value on each line
8482 (except possibly the first). Variant IDs are read from column #i and
8483 p-values are read from column #j, where i defaults to 1 and j defaults to
8484 i+1. The 'header' modifier causes the first nonempty line of this file
8485 to be skipped.
8486 * By default, --q-score-range errors out when a variant ID appears multiple
8487 times in the data file (and is also present in the main dataset). To use
8488 the minimum p-value in this case instead, add the 'min' modifier.
8489 --vscore-col-nums <...> : Process all the specified coefficient columns in
8490 the --variant-score file, identified by 1-based
8491 indexes and/or ranges of them.
8492 --parallel <k> <n> : Divide the output matrix into n pieces, and only compute
8493 the kth piece. The primary output file will have the
8494 piece number included in its name, e.g. plink2.king.13
8495 or plink2.king.13.zst if k is 13. Concatenating these
8496 files in order will yield the full matrix of interest.
8497 (Yes, this can be done before decompression.)
8498 N.B. This generally cannot be used to directly write a
8499 symmetric square matrix. Choose square0 or triangle
8500 shape instead, and postprocess as necessary.
8501 --memory <val> ['require'] : Set size, in MiB, of initial workspace malloc
8502 attempt. To error out instead of reducing the
8503 request size when the initial attempt fails, add
8504 the 'require' modifier.
8505 --threads <val> : Set maximum number of compute threads.
8506 --d <char> : Change variant/covariate range delimiter (normally '-').
8507 --seed <val...> : Set random number seed(s). Each value must be an
8508 integer between 0 and 4294967295 inclusive.
8509 Note that --threads and "--memory require" may also be
8510 needed to reproduce some randomized runs.
8511 --output-min-p <p> : Specify minimum p-value to write to reports. (2.23e-308
8512 is useful for preventing underflow in some programs.)
8513 --debug : Use slower, more crash-resistant logging method.
8514 --randmem : Randomize initial workspace memory (helps catch
8515 uninitialized-memory bugs).
8516 --warning-errcode : Return a nonzero error code to the OS when a run
8517 completes with warning(s).
8518 --zst-level <lvl> : Set the Zstd compression level (1-22, default 3).
8519
8520 Primary methods paper:
8521 Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015)
8522 Second-generation PLINK: rising to the challenge of larger and richer datasets.
8523 GigaScience, 4.
8524
8525
8526
8527 ]]></help>
8528 <citations>
8529 <citation type="doi">10.1186/s13742-015-0047-8</citation>
8530 <citation type="bibtex">@ARTICLE{Blankenberg20-plink,
8531 author = {Daniel Blankenberg Lab, et al},
8532 title = {In preparation..},
8533 }</citation>
8534 </citations>
8535 </tool>