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changeset 0:fb25b685d590 draft

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Initial wrapper upload.
author devteam
date Sat, 23 Nov 2013 16:12:29 -0500
parents
children e88ac3aabdc4
files test-data/regions.bed test-data/slice_in.vcf test-data/slice_out.vcf tool_dependencies.xml vcftools_slice.xml
diffstat 5 files changed, 171 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/regions.bed	Sat Nov 23 16:12:29 2013 -0500
@@ -0,0 +1,2 @@
+chr1	18960722	47767914
+chr1	65321419	85742338
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/slice_in.vcf	Sat Nov 23 16:12:29 2013 -0500
@@ -0,0 +1,76 @@
+##fileformat=VCFv4.1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	panc1_ng
+chr1	2985885	.	C	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:70:64:48:16:25%:9.8E-1:34:20:0:48:0:16
+chr1	3301721	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:687:619:205:414:66.77%:9.8E-1:35:24:130:75:279:135
+chr1	3328358	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:314:278:0:278:100%:9.8E-1:0:25:0:0:131:147
+chr1	3328659	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:417:362:294:68:18.78%:9.8E-1:35:19:110:184:35:33
+chr1	3329384	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:161:147:119:28:19.05%:9.8E-1:33:26:32:87:6:22
+chr1	3350409	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:567:471:157:314:66.67%:9.8E-1:33:25:75:82:180:134
+chr1	3352161	.	T	TA	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:511:467:362:105:22.29%:9.8E-1:34:33:167:195:59:46
+chr1	3352227	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:645:447:1:446:99.78%:9.8E-1:26:32:0:1:256:190
+chr1	3352347	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:517:427:0:427:100%:9.8E-1:0:34:0:0:126:301
+chr1	3352503	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:449:304:0:303:100%:9.8E-1:0:19:0:0:170:133
+chr1	3352541	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:466:401:0:401:100%:9.8E-1:0:25:0:0:189:212
+chr1	3352579	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:533:482:0:482:100%:9.8E-1:0:24:0:0:231:251
+chr1	3352763	.	CT	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:437:369:248:112:29.32%:9.8E-1:33:31:143:105:62:50
+chr1	3352784	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:443:357:253:104:29.05%:9.8E-1:30:25:160:93:54:50
+chr1	3352872	.	A	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:590:471:333:138:29.3%:9.8E-1:33:22:247:86:104:34
+chr1	3353890	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:478:430:0:429:99.77%:9.8E-1:0:34:0:0:242:187
+chr1	3353949	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:690:621:0:620:99.84%:9.8E-1:0:22:0:0:421:199
+chr1	3354595	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:519:461:3:458:99.35%:9.8E-1:30:19:0:3:197:261
+chr1	3354615	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:495:459:0:459:100%:9.8E-1:0:19:0:0:220:239
+chr1	18960722	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:701:648:489:159:24.54%:9.8E-1:34:22:346:143:121:38
+chr1	19071752	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:770:715:219:495:69.23%:9.8E-1:35:21:86:133:184:311
+chr1	19071865	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:517:479:174:305:63.54%:9.8E-1:35:34:42:132:91:214
+chr1	19072808	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:706:657:228:429:65.3%:9.8E-1:36:19:99:129:197:232
+chr1	19072926	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:673:618:183:435:70.39%:9.8E-1:35:24:96:87:187:248
+chr1	19074980	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:720:676:221:454:67.06%:9.8E-1:35:35:89:132:226:228
+chr1	19075225	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:718:660:190:468:70.91%:9.8E-1:34:34:93:97:231:237
+chr1	19075327	.	C	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:623:588:178:410:69.73%:9.8E-1:36:36:63:115:142:268
+chr1	36752152	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:845:780:216:564:72.31%:9.8E-1:36:25:103:113:249:315
+chr1	36759426	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:504:465:152:309:66.45%:9.8E-1:36:36:111:41:250:59
+chr1	36762396	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:468:377:0:377:100%:9.8E-1:0:19:0:0:127:250
+chr1	36770605	.	CTT	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:390:310:229:76:23.6%:9.8E-1:29:29:128:101:41:35
+chr1	40361783	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:533:505:33:471:93.27%:9.8E-1:35:24:9:24:206:265
+chr1	40363054	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:677:646:468:178:27.55%:9.8E-1:36:35:193:275:82:96
+chr1	43812075	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:692:639:16:621:97.18%:9.8E-1:33:20:10:6:343:278
+chr1	43814864	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:182:150:8:142:94.67%:9.8E-1:27:32:8:0:141:1
+chr1	45796269	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:571:534:0:534:100%:9.8E-1:0:24:0:0:111:423
+chr1	45798555	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:754:685:0:685:100%:9.8E-1:0:24:0:0:366:319
+chr1	45805566	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:327:276:0:276:100%:9.8E-1:0:20:0:0:127:149
+chr1	47682017	.	T	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:555:470:10:460:97.87%:9.8E-1:35:34:7:3:286:174
+chr1	47683201	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:708:660:195:465:70.45%:9.8E-1:35:24:83:112:218:247
+chr1	47684677	.	T	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:691:636:27:609:95.75%:9.8E-1:36:20:17:10:319:290
+chr1	47685455	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:407:343:0:343:99.71%:9.8E-1:0:23:0:0:46:297
+chr1	47691568	.	GCAGA	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:40:35:15:21:56.76%:9.8E-1:33:29:7:8:7:14
+chr1	47717189	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:714:667:201:464:69.57%:9.8E-1:36:21:115:86:242:222
+chr1	47726087	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:625:603:468:135:22.39%:9.8E-1:36:35:264:204:65:70
+chr1	47735280	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:414:381:98:283:74.28%:9.8E-1:35:36:74:24:225:58
+chr1	47767914	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:560:533:377:156:29.27%:9.8E-1:35:34:222:155:91:65
+chr1	51433821	.	G	GC	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:454:407:44:394:89.34%:9.8E-1:33:32:12:32:88:306
+chr1	51433863	.	G	GC	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:373:318:23:317:92.96%:9.8E-1:33:31:3:20:70:247
+chr1	51433888	.	A	AG	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:343:284:34:287:87.77%:9.8E-1:33:29:3:31:85:202
+chr1	51822188	.	GA	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:406:277:226:29:10.25%:9.8E-1:34:30:164:62:18:11
+chr1	51873951	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:773:740:521:219:29.59%:9.8E-1:37:37:189:332:88:131
+chr1	59248813	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:463:412:0:412:100%:9.8E-1:0:33:0:0:80:332
+chr1	59249031	.	T	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:284:249:0:249:100%:9.8E-1:0:22:0:0:103:146
+chr1	59249347	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:320:278:1:276:99.28%:9.8E-1:33:25:0:1:153:123
+chr1	65299551	.	G	GAATT	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:579:557:435:122:21.75%:9.8E-1:36:36:183:252:47:75
+chr1	65301238	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:408:386:130:256:66.32%:9.8E-1:37:35:23:107:41:215
+chr1	65310489	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:754:714:553:161:22.55%:9.8E-1:35:35:287:266:98:63
+chr1	65311214	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:788:738:275:463:62.74%:9.8E-1:35:24:129:146:236:227
+chr1	65321250	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:808:739:283:456:61.71%:9.8E-1:34:20:140:143:236:220
+chr1	65321388	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:542:506:30:476:94.07%:9.8E-1:36:20:4:26:142:334
+chr1	65321419	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:471:426:131:294:69.01%:9.8E-1:35:19:27:104:51:243
+chr1	65325970	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:491:457:40:417:91.25%:9.8E-1:35:36:8:32:82:335
+chr1	65330682	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:482:448:141:307:68.53%:9.8E-1:35:21:21:120:41:266
+chr1	65335095	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:1022:957:364:593:61.96%:9.8E-1:35:21:147:217:251:342
+chr1	85732065	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:319:295:6:289:97.97%:9.8E-1:37:36:5:1:206:83
+chr1	85732133	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:434:405:124:281:69.21%:9.8E-1:36:24:82:42:200:81
+chr1	85732941	.	A	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:479:423:9:414:97.64%:9.8E-1:37:35:2:7:127:287
+chr1	85741921	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:239:218:10:208:95.41%:9.8E-1:34:25:8:2:172:36
+chr1	85742012	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:484:437:302:135:30.89%:9.8E-1:35:34:175:127:70:65
+chr1	85742338	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:260:216:6:210:97.22%:9.8E-1:30:23:1:5:52:158
+chr1	110882444	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:247:223:76:147:65.92%:9.8E-1:32:25:39:37:80:67
+chr1	110883569	.	A	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:635:585:186:399:68.21%:9.8E-1:34:34:100:86:196:203
+chr1	114936079	.	T	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:375:318:257:61:19.18%:9.8E-1:36:17:108:149:38:23
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/slice_out.vcf	Sat Nov 23 16:12:29 2013 -0500
@@ -0,0 +1,38 @@
+##fileformat=VCFv4.1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	panc1_ng
+chr1	19071752	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:770:715:219:495:69.23%:9.8E-1:35:21:86:133:184:311
+chr1	19071865	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:517:479:174:305:63.54%:9.8E-1:35:34:42:132:91:214
+chr1	19072808	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:706:657:228:429:65.3%:9.8E-1:36:19:99:129:197:232
+chr1	19072926	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:673:618:183:435:70.39%:9.8E-1:35:24:96:87:187:248
+chr1	19074980	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:720:676:221:454:67.06%:9.8E-1:35:35:89:132:226:228
+chr1	19075225	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:718:660:190:468:70.91%:9.8E-1:34:34:93:97:231:237
+chr1	19075327	.	C	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:623:588:178:410:69.73%:9.8E-1:36:36:63:115:142:268
+chr1	36752152	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:845:780:216:564:72.31%:9.8E-1:36:25:103:113:249:315
+chr1	36759426	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:504:465:152:309:66.45%:9.8E-1:36:36:111:41:250:59
+chr1	36762396	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:468:377:0:377:100%:9.8E-1:0:19:0:0:127:250
+chr1	36770605	.	CTT	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:390:310:229:76:23.6%:9.8E-1:29:29:128:101:41:35
+chr1	40361783	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:533:505:33:471:93.27%:9.8E-1:35:24:9:24:206:265
+chr1	40363054	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:677:646:468:178:27.55%:9.8E-1:36:35:193:275:82:96
+chr1	43812075	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:692:639:16:621:97.18%:9.8E-1:33:20:10:6:343:278
+chr1	43814864	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:182:150:8:142:94.67%:9.8E-1:27:32:8:0:141:1
+chr1	45796269	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:571:534:0:534:100%:9.8E-1:0:24:0:0:111:423
+chr1	45798555	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:754:685:0:685:100%:9.8E-1:0:24:0:0:366:319
+chr1	45805566	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:327:276:0:276:100%:9.8E-1:0:20:0:0:127:149
+chr1	47682017	.	T	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:555:470:10:460:97.87%:9.8E-1:35:34:7:3:286:174
+chr1	47683201	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:708:660:195:465:70.45%:9.8E-1:35:24:83:112:218:247
+chr1	47684677	.	T	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:691:636:27:609:95.75%:9.8E-1:36:20:17:10:319:290
+chr1	47685455	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:407:343:0:343:99.71%:9.8E-1:0:23:0:0:46:297
+chr1	47691568	.	GCAGA	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:40:35:15:21:56.76%:9.8E-1:33:29:7:8:7:14
+chr1	47717189	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:714:667:201:464:69.57%:9.8E-1:36:21:115:86:242:222
+chr1	47726087	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:625:603:468:135:22.39%:9.8E-1:36:35:264:204:65:70
+chr1	47735280	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:414:381:98:283:74.28%:9.8E-1:35:36:74:24:225:58
+chr1	47767914	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:560:533:377:156:29.27%:9.8E-1:35:34:222:155:91:65
+chr1	65325970	.	C	T	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:491:457:40:417:91.25%:9.8E-1:35:36:8:32:82:335
+chr1	65330682	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:482:448:141:307:68.53%:9.8E-1:35:21:21:120:41:266
+chr1	65335095	.	T	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:1022:957:364:593:61.96%:9.8E-1:35:21:147:217:251:342
+chr1	85732065	.	A	G	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:319:295:6:289:97.97%:9.8E-1:37:36:5:1:206:83
+chr1	85732133	.	G	A	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:434:405:124:281:69.21%:9.8E-1:36:24:82:42:200:81
+chr1	85732941	.	A	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:479:423:9:414:97.64%:9.8E-1:37:35:2:7:127:287
+chr1	85741921	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:239:218:10:208:95.41%:9.8E-1:34:25:8:2:172:36
+chr1	85742012	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:484:437:302:135:30.89%:9.8E-1:35:34:175:127:70:65
+chr1	85742338	.	G	C	.	PASS	.	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:0:260:216:6:210:97.22%:9.8E-1:30:23:1:5:52:158
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Nov 23 16:12:29 2013 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vcftools" version="0.1.11">
+        <repository changeset_revision="a44e7b401f4f" name="package_vcftools_0_1_11" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcftools_slice.xml	Sat Nov 23 16:12:29 2013 -0500
@@ -0,0 +1,49 @@
+<tool id="vcftools_slice" name="Slice VCF" version="0.1">
+    <description>to get data from selected regions</description>
+
+    <requirements>
+        <requirement type="package">vcftools</requirement>
+    </requirements>
+    
+    <command>
+        ## Only works if input is sorted.
+        vcf-sort ${input} > sorted.vcf
+
+        ## As of v0.1.10, the first line of a BED file is assumed to be a header and ignored,
+        ## so add a dummy header line if necessary.
+        #set first_line = open( str($regions) ).readline()
+        #if first_line.startswith( '#' ):
+            ## Header already exists, so just link.
+            ; ln -s $regions regions.bed
+        #else:
+            ## Add dummy header.
+            ; echo '#dummy header' | cat - $regions > regions.bed
+        #end if
+
+        ## Slice VCF.
+        ; vcftools --vcf sorted.vcf --out output --bed regions.bed --recode
+    </command>
+    
+    <inputs>
+        <param name="input" label="Input dataset" type="data" format="vcf"/>
+        <param name="regions" label="Regions" type="data" format="bed"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="vcf" from_work_dir="output.recode.vcf"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="slice_in.vcf"/>
+            <param name="regions" value="regions.bed"/>
+            <output name="output" file="slice_out.vcf"/>
+        </test>
+    </tests>
+
+    <help>
+        Please see the VCFtools `documentation`__ for help and further information.
+
+        .. __: http://vcftools.sourceforge.net/docs.html
+    </help>
+</tool>