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comparison dir_plugins/plugin_config.txt @ 0:e545d0a25ffe draft

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author dvanzessen
date Mon, 15 Jul 2019 05:17:17 -0400
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1 my $VEP_PLUGIN_CONFIG = {
2 "plugins" => [
3
4 ## PATHOGENICITY PREDICTIONS
5 ############################
6
7 # dbNSFP
8 # https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm
9 # Requires tabix-indexed data file as first param
10 # Field names are listed below and rendered as a multi-selectable autocomplete text field
11 # Human, GRCh38 only (3.x), for GRCh37 use 2.9.x
12 {
13 "key" => "dbNSFP",
14 "label" => "dbNSFP",
15 "available" => 0,
16 "enabled" => 0,
17 "section" => "Pathogenicity predictions",
18 "helptip" => "dbNSFP provides pathogenicity predictions for missense variants from various algorithms",
19 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/dbNSFP.pm",
20 "requires_data" => 1,
21 "requires_install" => 1,
22 "params" => [
23 #"/path/to/dbNSFP3.5a.txt.gz",
24 "@*"
25 ],
26 "species" => [
27 "homo_sapiens"
28 ],
29 "form" => [
30 {
31 "name" => "dbNSFP_fields",
32 "label" => "Fields to include",
33 "helptip" => "Fields to fetch from dbNSFP; hold down the Ctrl (Windows) / Command (Mac) button to select multiple options",
34 "value" => "",
35 'type' => 'dropdown',
36 'multiple' => 1,
37 'style' => 'height:150px',
38 'required' => 1,
39 'notes' => 'Field descriptions in <a rel="external" href="https://drive.google.com/file/d/0B60wROKy6OqcNGJ2STJlMTJONk0/view">dbNSFP README</a>',
40 # "class" => "jquery-multiselect",
41 "values" => [
42 # "chr",
43 # "pos(1-based)",
44 # "ref",
45 # "alt",
46 # "aaref",
47 # "aaalt",
48 # "rs_dbSNP150",
49 # "hg19_chr",
50 # "hg19_pos(1-based)",
51 # "hg18_chr",
52 # "hg18_pos(1-based)",
53 # "genename",
54 # "cds_strand",
55 # "refcodon",
56 # "codonpos",
57 "codon_degeneracy",
58 "Ancestral_allele",
59 "AltaiNeandertal",
60 "Denisova",
61 # "Ensembl_geneid",
62 # "Ensembl_transcriptid",
63 # "Ensembl_proteinid",
64 # "aapos",
65 # "SIFT_score",
66 # "SIFT_converted_rankscore",
67 # "SIFT_pred",
68 # "Uniprot_acc_Polyphen2",
69 # "Uniprot_id_Polyphen2",
70 # "Uniprot_aapos_Polyphen2",
71 # "Polyphen2_HDIV_score",
72 # "Polyphen2_HDIV_rankscore",
73 # "Polyphen2_HDIV_pred",
74 # "Polyphen2_HVAR_score",
75 # "Polyphen2_HVAR_rankscore",
76 # "Polyphen2_HVAR_pred",
77 "LRT_score",
78 "LRT_converted_rankscore",
79 "LRT_pred",
80 "LRT_Omega",
81 "MutationTaster_score",
82 "MutationTaster_converted_rankscore",
83 "MutationTaster_pred",
84 "MutationTaster_model",
85 "MutationTaster_AAE",
86 "MutationAssessor_UniprotID",
87 "MutationAssessor_variant",
88 "MutationAssessor_score",
89 "MutationAssessor_score_rankscore",
90 "MutationAssessor_pred",
91 "FATHMM_score",
92 "FATHMM_converted_rankscore",
93 "FATHMM_pred",
94 "PROVEAN_score",
95 "PROVEAN_converted_rankscore",
96 "PROVEAN_pred",
97 "Transcript_id_VEST3",
98 "Transcript_var_VEST3",
99 "VEST3_score",
100 "VEST3_rankscore",
101 "MetaSVM_score",
102 "MetaSVM_rankscore",
103 "MetaSVM_pred",
104 "MetaLR_score",
105 "MetaLR_rankscore",
106 "MetaLR_pred",
107 "Reliability_index",
108 "M-CAP_score",
109 "M-CAP_rankscore",
110 "M-CAP_pred",
111 "REVEL_score",
112 "REVEL_rankscore",
113 "MutPred_score",
114 "MutPred_rankscore",
115 "MutPred_protID",
116 "MutPred_AAchange",
117 "MutPred_Top5features",
118 "CADD_raw",
119 "CADD_raw_rankscore",
120 "CADD_phred",
121 "DANN_score",
122 "DANN_rankscore",
123 "fathmm-MKL_coding_score",
124 "fathmm-MKL_coding_rankscore",
125 "fathmm-MKL_coding_pred",
126 "fathmm-MKL_coding_group",
127 "Eigen_coding_or_noncoding",
128 "Eigen-raw",
129 "Eigen-phred",
130 "Eigen-PC-raw",
131 "Eigen-PC-phred",
132 "Eigen-PC-raw_rankscore",
133 "GenoCanyon_score",
134 "GenoCanyon_score_rankscore",
135 "integrated_fitCons_score",
136 "integrated_fitCons_score_rankscore",
137 "integrated_confidence_value",
138 "GM12878_fitCons_score",
139 "GM12878_fitCons_score_rankscore",
140 "GM12878_confidence_value",
141 "H1-hESC_fitCons_score",
142 "H1-hESC_fitCons_score_rankscore",
143 "H1-hESC_confidence_value",
144 "HUVEC_fitCons_score",
145 "HUVEC_fitCons_score_rankscore",
146 "HUVEC_confidence_value",
147 "GERP++_NR",
148 "GERP++_RS",
149 "GERP++_RS_rankscore",
150 "phyloP100way_vertebrate",
151 "phyloP100way_vertebrate_rankscore",
152 "phyloP20way_mammalian",
153 "phyloP20way_mammalian_rankscore",
154 "phastCons100way_vertebrate",
155 "phastCons100way_vertebrate_rankscore",
156 "phastCons20way_mammalian",
157 "phastCons20way_mammalian_rankscore",
158 "SiPhy_29way_pi",
159 "SiPhy_29way_logOdds",
160 "SiPhy_29way_logOdds_rankscore",
161 "1000Gp3_AC",
162 "1000Gp3_AF",
163 "1000Gp3_AFR_AC",
164 "1000Gp3_AFR_AF",
165 "1000Gp3_EUR_AC",
166 "1000Gp3_EUR_AF",
167 "1000Gp3_AMR_AC",
168 "1000Gp3_AMR_AF",
169 "1000Gp3_EAS_AC",
170 "1000Gp3_EAS_AF",
171 "1000Gp3_SAS_AC",
172 "1000Gp3_SAS_AF",
173 "TWINSUK_AC",
174 "TWINSUK_AF",
175 "ALSPAC_AC",
176 "ALSPAC_AF",
177 "ESP6500_AA_AC",
178 "ESP6500_AA_AF",
179 "ESP6500_EA_AC",
180 "ESP6500_EA_AF",
181 "ExAC_AC",
182 "ExAC_AF",
183 "ExAC_Adj_AC",
184 "ExAC_Adj_AF",
185 "ExAC_AFR_AC",
186 "ExAC_AFR_AF",
187 "ExAC_AMR_AC",
188 "ExAC_AMR_AF",
189 "ExAC_EAS_AC",
190 "ExAC_EAS_AF",
191 "ExAC_FIN_AC",
192 "ExAC_FIN_AF",
193 "ExAC_NFE_AC",
194 "ExAC_NFE_AF",
195 "ExAC_SAS_AC",
196 "ExAC_SAS_AF",
197 "ExAC_nonTCGA_AC",
198 "ExAC_nonTCGA_AF",
199 "ExAC_nonTCGA_Adj_AC",
200 "ExAC_nonTCGA_Adj_AF",
201 "ExAC_nonTCGA_AFR_AC",
202 "ExAC_nonTCGA_AFR_AF",
203 "ExAC_nonTCGA_AMR_AC",
204 "ExAC_nonTCGA_AMR_AF",
205 "ExAC_nonTCGA_EAS_AC",
206 "ExAC_nonTCGA_EAS_AF",
207 "ExAC_nonTCGA_FIN_AC",
208 "ExAC_nonTCGA_FIN_AF",
209 "ExAC_nonTCGA_NFE_AC",
210 "ExAC_nonTCGA_NFE_AF",
211 "ExAC_nonTCGA_SAS_AC",
212 "ExAC_nonTCGA_SAS_AF",
213 "ExAC_nonpsych_AC",
214 "ExAC_nonpsych_AF",
215 "ExAC_nonpsych_Adj_AC",
216 "ExAC_nonpsych_Adj_AF",
217 "ExAC_nonpsych_AFR_AC",
218 "ExAC_nonpsych_AFR_AF",
219 "ExAC_nonpsych_AMR_AC",
220 "ExAC_nonpsych_AMR_AF",
221 "ExAC_nonpsych_EAS_AC",
222 "ExAC_nonpsych_EAS_AF",
223 "ExAC_nonpsych_FIN_AC",
224 "ExAC_nonpsych_FIN_AF",
225 "ExAC_nonpsych_NFE_AC",
226 "ExAC_nonpsych_NFE_AF",
227 "ExAC_nonpsych_SAS_AC",
228 "ExAC_nonpsych_SAS_AF",
229 "gnomAD_exomes_AC",
230 "gnomAD_exomes_AN",
231 "gnomAD_exomes_AF",
232 "gnomAD_exomes_AFR_AC",
233 "gnomAD_exomes_AFR_AN",
234 "gnomAD_exomes_AFR_AF",
235 "gnomAD_exomes_AMR_AC",
236 "gnomAD_exomes_AMR_AN",
237 "gnomAD_exomes_AMR_AF",
238 "gnomAD_exomes_ASJ_AC",
239 "gnomAD_exomes_ASJ_AN",
240 "gnomAD_exomes_ASJ_AF",
241 "gnomAD_exomes_EAS_AC",
242 "gnomAD_exomes_EAS_AN",
243 "gnomAD_exomes_EAS_AF",
244 "gnomAD_exomes_FIN_AC",
245 "gnomAD_exomes_FIN_AN",
246 "gnomAD_exomes_FIN_AF",
247 "gnomAD_exomes_NFE_AC",
248 "gnomAD_exomes_NFE_AN",
249 "gnomAD_exomes_NFE_AF",
250 "gnomAD_exomes_SAS_AC",
251 "gnomAD_exomes_SAS_AN",
252 "gnomAD_exomes_SAS_AF",
253 "gnomAD_exomes_OTH_AC",
254 "gnomAD_exomes_OTH_AN",
255 "gnomAD_exomes_OTH_AF",
256 "gnomAD_genomes_AC",
257 "gnomAD_genomes_AN",
258 "gnomAD_genomes_AF",
259 "gnomAD_genomes_AFR_AC",
260 "gnomAD_genomes_AFR_AN",
261 "gnomAD_genomes_AFR_AF",
262 "gnomAD_genomes_AMR_AC",
263 "gnomAD_genomes_AMR_AN",
264 "gnomAD_genomes_AMR_AF",
265 "gnomAD_genomes_ASJ_AC",
266 "gnomAD_genomes_ASJ_AN",
267 "gnomAD_genomes_ASJ_AF",
268 "gnomAD_genomes_EAS_AC",
269 "gnomAD_genomes_EAS_AN",
270 "gnomAD_genomes_EAS_AF",
271 "gnomAD_genomes_FIN_AC",
272 "gnomAD_genomes_FIN_AN",
273 "gnomAD_genomes_FIN_AF",
274 "gnomAD_genomes_NFE_AC",
275 "gnomAD_genomes_NFE_AN",
276 "gnomAD_genomes_NFE_AF",
277 "gnomAD_genomes_OTH_AC",
278 "gnomAD_genomes_OTH_AN",
279 "gnomAD_genomes_OTH_AF",
280 "clinvar_rs",
281 "clinvar_clnsig",
282 "clinvar_trait",
283 "clinvar_golden_stars",
284 "Interpro_domain",
285 "GTEx_V6p_gene",
286 "GTEx_V6p_tissue"
287 ],
288 },
289 ]
290 },
291
292 # CADD
293 # https://github.com/ensembl-variation/VEP_plugins/blob/master/CADD.pm
294 # Requires tabix-indexed data file as first param
295 # No other parameters so no form required
296 # data file currently only available for GRCh37
297 {
298 "key" => "CADD",
299 "label" => "CADD",
300 "available" => 0,
301 "enabled" => 0,
302 "section" => "Pathogenicity predictions",
303 "helptip" => "Combined Annotation Dependent Depletion (CADD) is a tool for scoring the deleteriousness of single nucleotide variants and insertion/deletion variants in the human genome. CADD integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations.",
304 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/CADD.pm",
305 "requires_data" => 1,
306 "species" => [
307 "homo_sapiens"
308 ],
309 "params" => [
310 #"/path/to/whole_genome_SNVs.tsv.gz"
311 ]
312 },
313
314 # FATHMM-MKL
315 # https://github.com/ensembl-variation/VEP_plugins/blob/master/FATHMM_MKL.pm
316 # Requires tabix-indexed data file as first param
317 # No other parameters so no form required
318 # data file currently only available for GRCh37
319 {
320 "key" => "FATHMM_MKL",
321 "label" => "FATHMM-MKL",
322 "available" => 0,
323 "enabled" => 0,
324 "section" => "Pathogenicity predictions",
325 "helptip" => "FATHMM-MKL predicts functional consequences of variants, both coding and non-coding.",
326 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/FATHMM_MKL.pm",
327 "requires_data" => 1,
328 "species" => [
329 "homo_sapiens"
330 ],
331 "params" => [
332 #"/path/to/fathmm-MKL_Current.tab.gz"
333 ]
334 },
335
336 # GWAVA
337 # https://www.sanger.ac.uk/sanger/StatGen_Gwava
338 # Requires tabix-indexed BED data file from ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/
339 # data file currently only available for GRCh37
340 {
341 "key" => "Gwava",
342 "label" => "GWAVA",
343 "available" => 0,
344 "enabled" => 0,
345 "section" => "Pathogenicity predictions",
346 "helptip" => "Retrieves precomputed Genome Wide Annotation of VAriants (GWAVA) scores for any variant that overlaps a known variant from the Ensembl variation database",
347 "plugin_url" => "ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/Gwava.pm",
348 "requires_data" => 1,
349 "species" => [
350 "homo_sapiens"
351 ],
352 "params" => [
353 "@*",
354 # "/path/to/gwava_scores.bed.gz"
355 ],
356 "form" => [
357 {
358 "name" => "model",
359 "label" => "Model",
360 "type" => "dropdown",
361 "values" => [
362 { "value" => "region", "caption" => "Region" },
363 { "value" => "tss", "caption" => "TSS" },
364 { "value" => "unmatched", "caption" => "Unmatched" }
365 ],
366 "value" => "region",
367 },
368 ],
369 },
370
371 # Carol
372 # https://github.com/ensembl-variation/VEP_plugins/blob/master/Carol.pm
373 # Requires Math/CDF Perl module
374 {
375 "key" => "Carol",
376 "helptip" => "Calculates the Combined Annotation scoRing toOL (CAROL) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
377 "available" => 0,
378 "enabled" => 0,
379 "section" => "Pathogenicity predictions",
380 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Carol.pm",
381 "requires_install" => 1,
382 "species" => [
383 "homo_sapiens"
384 ],
385 },
386
387 # Condel
388 # https://github.com/ensembl-variation/VEP_plugins/blob/master/Condel.pm
389 # Requires path to config directory as first param
390 # config directory is checked out as part of VEP_plugins repo, as /[path]/VEP_plugins/config/Condel/config
391 # Within that dir, edit condel_SP.conf so that condel.dir points to /[path]/VEP_plugins/config/Condel
392 {
393 "key" => "Condel",
394 "helptip" => "Calculates the Consensus Deleteriousness (Condel) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
395 "available" => 0,
396 "enabled" => 0,
397 "section" => "Pathogenicity predictions",
398 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Condel.pm",
399 "requires_install" => 1,
400 "species" => [
401 "homo_sapiens"
402 ],
403 "params" => [
404 # "/path/to/config/Condel/config",
405 "@*"
406 ],
407 "form" => [
408 {
409 "name" => "score_pred",
410 "label" => "Score/prediction",
411 "type" => "dropdown",
412 "values" => [
413 { "value" => "b", "caption" => "Prediction and score" },
414 { "value" => "p", "caption" => "Prediction only" },
415 { "value" => "s", "caption" => "Score only" }
416 ],
417 "value" => "b",
418 },
419 ],
420 },
421
422 # LOFTEE
423 # See https://github.com/konradjk/loftee for details
424 {
425 "key" => "LoF",
426 "helptip" => "LOFTEE identifies LoF (loss-of-function) variation",
427 "available" => 0,
428 "enabled" => 0,
429 "section" => "Pathogenicity predictions",
430 "plugin_url" => "https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm",
431 "requires_data" => 1,
432 "requires_install" => 1,
433 "params" => [
434 "@*"
435 ]
436 },
437
438 # LoFtool
439 # Requires LoFtool_scores.txt file as first param (available in VEP_plugins GitHub repo)
440 {
441 "key" => "LoFtool",
442 "helptip" => "Provides a per-gene rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations in ExAC data",
443 "available" => 0,
444 "enabled" => 0,
445 "section" => "Pathogenicity predictions",
446 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LoFtool.pm",
447 "requires_data" => 1,
448 "species" => [
449 "homo_sapiens"
450 ],
451 "params" => [
452 # "/path/to/LoFtool_scores.txt"
453 ]
454 },
455
456 # ExACpLI
457 # Requires ExACpLI_values.txt file as first param (available in VEP_plugins GitHub repo)
458 {
459 "key" => "ExACpLI",
460 "helptip" => "Provides a per-gene probability of being loss-of-function intolerant (pLI) from ExAC data",
461 "available" => 0,
462 "enabled" => 0,
463 "section" => "Pathogenicity predictions",
464 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/ExACpLI.pm",
465 "requires_data" => 1,
466 "species" => [
467 "homo_sapiens"
468 ],
469 "params" => [
470 # "/path/to/ExACpLI_values.txt"
471 ]
472 },
473
474 # MPC
475 # Requires fordist_constraint_official_mpc_values.txt.gz data file
476 {
477 "key" => "MPC",
478 "helptip" => "MPC is a missense deleteriousness metric based on the analysis of genic regions depleted of missense mutations in ExAC",
479 "available" => 0,
480 "enabled" => 0,
481 "section" => "Pathogenicity predictions",
482 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/MPC.pm",
483 "requires_data" => 1,
484 "species" => [
485 "homo_sapiens"
486 ],
487 "params" => [
488 # "/path/to/fordist_constraint_official_mpc_values.txt.gz"
489 ]
490 },
491
492 # MTR
493 # Requires mtrflatfile_1.0.txt.gz data file from ftp://mtr-viewer.mdhs.unimelb.edu.au/pub
494 {
495 "key" => "MTR",
496 "helptip" => "MTR scores quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence",
497 "available" => 0,
498 "enabled" => 0,
499 "section" => "Pathogenicity predictions",
500 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/MTR.pm",
501 "requires_data" => 1,
502 "species" => [
503 "homo_sapiens"
504 ],
505 "params" => [
506 # "/path/to/mtrflatfile_1.0.txt.gz"
507 ]
508 },
509
510 # REVEL
511 # Requires data file processed from revel_all_chromosomes.csv.zip
512 {
513 "key" => "REVEL",
514 "helptip" => "An ensemble method for predicting the pathogenicity of rare missense variants",
515 "available" => 0,
516 "enabled" => 0,
517 "section" => "Pathogenicity predictions",
518 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/REVEL.pm",
519 "requires_data" => 1,
520 "species" => [
521 "homo_sapiens"
522 ],
523 "params" => [
524 # "/path/to/revel_all_chromosomes.tsv.gz"
525 ]
526 },
527
528
529
530 ## SPLICING PREDICTIONS
531 #######################
532
533 # dbscSNV
534 {
535 "key" => "dbscSNV",
536 "label" => "dbscSNV",
537 "available" => 0,
538 "enabled" => 0,
539 "section" => "Splicing predictions",
540 "helptip" => "Retrieves data for splicing variants from a tabix-indexed dbscSNV file",
541 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/dbscSNV.pm",
542 "requires_data" => 1,
543 "requires_install" => 1,
544 "params" => [
545 #"/path/to/dbscSNV1.1.txt.gz"
546 ],
547 "species" => [
548 "homo_sapiens"
549 ],
550 },
551
552 # GeneSplicer
553 {
554 "key" => "GeneSplicer",
555 "label" => "GeneSplicer",
556 "helptip" => "Detects splice sites in genomic DNA",
557 "available" => 0,
558 "enabled" => 0,
559 "section" => "Splicing predictions",
560 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/GeneSplicer.pm",
561 "requires_install" => 1,
562 "species" => [
563 "homo_sapiens"
564 ],
565 "params" => [
566 #"/path/to/genesplicer/bin/linux/genesplicer",
567 #"/path/to/genesplicer/human",
568 "@*"
569 ]
570 },
571
572 # MaxEntScan
573 {
574 "key" => "MaxEntScan",
575 "label" => "MaxEntScan",
576 "helptip" => "Sequence motif and maximum entropy based splice site consensus predictions",
577 "available" => 0,
578 "enabled" => 0,
579 "section" => "Splicing predictions",
580 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/MaxEntScan.pm",
581 "requires_install" => 1,
582 "species" => [
583 "homo_sapiens"
584 ],
585 "params" => [
586 #"/path/to/maxentscan"
587 ]
588 },
589
590 # SpliceRegion
591 {
592 "key" => "SpliceRegion",
593 "label" => "SpliceRegion",
594 "helptip" => "More granular predictions of splicing effects",
595 "available" => 0,
596 "enabled" => 0,
597 "section" => "Splicing predictions",
598 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/SpliceRegion.pm",
599 },
600
601
602 ## CONSERVATION
603 ###############
604
605 # Blosum62
606 {
607 "key" => "Blosum62",
608 "label" => "BLOSUM62",
609 "helptip" => "BLOSUM62 amino acid conservation score",
610 "available" => 0,
611 "enabled" => 0,
612 "section" => "Conservation",
613 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Blosum62.pm",
614 },
615
616 # Conservation
617 # Use the following query to get valid species sets:
618 #
619 # SELECT group_concat(concat("_stt_", gd.name) SEPARATOR ' '), REPLACE(mlss.name, "Gerp Conservation Scores ", ""), sst.value
620 # FROM method_link ml,
621 # method_link_species_set mlss,
622 # genome_db gd, species_set ss, species_set_tag sst
623 # WHERE mlss.method_link_id = ml.method_link_id AND
624 # mlss.species_set_id = ss.species_set_id AND
625 # ss.genome_db_id = gd.genome_db_id AND
626 # ss.species_set_id = sst.species_set_id AND
627 # (ml.class = "ConservationScore.conservation_score")
628 # GROUP BY mlss.species_set_id
629 {
630 "key" => "Conservation",
631 "helptip" => "Retrieves a conservation score from the Ensembl Compara databases for variant positions",
632 "available" => 0,
633 "enabled" => 0,
634 "section" => "Conservation",
635 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Conservation.pm",
636 "params" => [
637 "@*"
638 ],
639 "form" => [
640 {
641 "name" => "method_link_type",
642 "label" => "Method",
643 "type" => "dropdown",
644 "values" => [
645 { "value" => "GERP_CONSERVATION_SCORE", "caption" => "GERP"}
646 ]
647 },
648 {
649 "name" => "species_set",
650 "label" => "Species set",
651 "type" => "dropdown",
652 "values" => [
653 { "value" => "mammals", "caption" => "39 eutherian mammals" }, #"class" => "_stt_macaca_mulatta _stt_echinops_telfairi _stt_tupaia_belangeri _stt_erinaceus_europaeus _stt_sorex_araneus _stt_microcebus_murinus _stt_pongo_abelii _stt_equus_caballus _stt_ochotona_princeps _stt_cavia_porcellus _stt_choloepus_hoffmanni _stt_procavia_capensis _stt_tursiops_truncatus _stt_tarsius_syrichta _stt_dipodomys_ordii _stt_vicugna_pacos _stt_pteropus_vampyrus _stt_loxodonta_africana _stt_oryctolagus_cuniculus _stt_ailuropoda_melanoleuca _stt_nomascus_leucogenys _stt_callithrix_jacchus _stt_myotis_lucifugus _stt_bos_taurus _stt_gorilla_gorilla _stt_otolemur_garnettii _stt_pan_troglodytes _stt_ictidomys_tridecemlineatus _stt_sus_scrofa _stt_mus_musculus _stt_canis_familiaris _stt_mustela_putorius_furo _stt_felis_catus _stt_ovis_aries _stt_dasypus_novemcinctus _stt_homo_sapiens _stt_papio_anubis _stt_chlorocebus_sabaeus _stt_rattus_norvegicus" },
654 { "value" => "amniotes", "caption" => "23 amniota vertebrates" }, #"class" => "_stt_macaca_mulatta _stt_ornithorhynchus_anatinus _stt_monodelphis_domestica _stt_pongo_abelii _stt_equus_caballus _stt_taeniopygia_guttata _stt_oryctolagus_cuniculus _stt_anolis_carolinensis _stt_meleagris_gallopavo _stt_callithrix_jacchus _stt_bos_taurus _stt_gorilla_gorilla _stt_pan_troglodytes _stt_sus_scrofa _stt_mus_musculus _stt_canis_familiaris _stt_felis_catus _stt_gallus_gallus _stt_ovis_aries _stt_homo_sapiens _stt_papio_anubis _stt_chlorocebus_sabaeus _stt_rattus_norvegicus" },
655 { "value" => "sauropsids", "caption" => "7 sauropsids" }, #"class" => "_stt_taeniopygia_guttata _stt_anolis_carolinensis _stt_meleagris_gallopavo _stt_pelodiscus_sinensis _stt_gallus_gallus _stt_anas_platyrhynchos _stt_ficedula_albicollis" },
656 { "value" => "fish", "caption" => "11 fish" }, #"class" => "_stt_takifugu_rubripes _stt_gasterosteus_aculeatus _stt_oryzias_latipes _stt_tetraodon_nigroviridis _stt_gadus_morhua _stt_oreochromis_niloticus _stt_xiphophorus_maculatus _stt_astyanax_mexicanus _stt_lepisosteus_oculatus _stt_poecilia_formosa _stt_danio_rerio" },
657 ]
658 },
659 ]
660 },
661
662 # AncestralAllele
663 # Requires processed FASTA file from ftp://ftp.ensembl.org/pub/current_fasta/ancestral_alleles/
664 {
665 "key" => "AncestralAllele",
666 "label" => "Ancestral allele",
667 "helptip" => "Retrieves the ancestral allele for variants inferred from the Ensembl Compara Enredo-Pecan-Ortheus (EPO) pipeline",
668 "available" => 0,
669 "enabled" => 0,
670 "section" => "Conservation",
671 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/AncestralAllele.pm",
672 "requires_data" => 1,
673 "species" => [
674 "homo_sapiens"
675 ],
676 "params" => [
677 # "/path/to/homo_sapiens_ancestor_GRCh38_e93.fa.gz"
678 ]
679 },
680
681
682 ## FREQUENCY DATA
683 #################
684
685 # ExAC
686 {
687 "key" => "ExAC",
688 "label" => "ExAC frequencies",
689 "helptip" => "Reports allele frequencies from the Exome Aggregation Consortium",
690 "available" => 0,
691 "enabled" => 0,
692 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/ExAC.pm",
693 "section" => "Frequency data",
694 "requires_data" => 1,
695 "species" => [
696 "homo_sapiens"
697 ],
698 "params" => [
699 # "/path/to/ExAC.r0.3.sites.vep.vcf.gz"
700 ]
701 },
702
703
704 ## OTHER
705 ########
706
707 # CSN
708 {
709 "key" => "CSN",
710 "helptip" => "Reports Clinical Sequencing Nomenclature (CSN) for variants",
711 "available" => 0,
712 "enabled" => 0,
713 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/CSN.pm",
714 },
715
716 # miRNA
717 {
718 "key" => "miRNA",
719 "label" => "miRNA structure",
720 "helptip" => "Determines where in the secondary structure of a miRNA a variant falls",
721 "available" => 0,
722 "enabled" => 0,
723 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/miRNA.pm",
724 },
725
726
727
728 # NearestGene
729 {
730 "key" => "NearestGene",
731 "label" => "Nearest gene",
732 "helptip" => "Finds the nearest gene to non-genic variants",
733 "available" => 0,
734 "enabled" => 0,
735 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/NearestGene.pm",
736 },
737
738 # LD
739 {
740 "key" => "LD",
741 "label" => "Linkage disequilibrium",
742 "helptip" => "Finds variants in linkage disequilibrium with any overlapping existing variants from the Ensembl variation databases",
743 "available" => 0,
744 "enabled" => 0,
745 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LD.pm",
746 "section" => "Variant data",
747 "params" => [
748 "@*"
749 ],
750 "form" => [
751 {
752 "name" => "population",
753 "label" => "Population",
754 "type" => "dropdown",
755 "values" => [
756 { "value" => "1000GENOMES:phase_3:ACB", "caption" => "African Caribbean in Barbados" },
757 { "value" => "1000GENOMES:phase_3:ASW", "caption" => "African Ancestry in Southwest US" },
758 { "value" => "1000GENOMES:phase_3:BEB", "caption" => "Bengali in Bangladesh" },
759 { "value" => "1000GENOMES:phase_3:CDX", "caption" => "Chinese Dai in Xishuangbanna, China" },
760 { "value" => "1000GENOMES:phase_3:CEU", "caption" => "Utah residents with Northern and Western European ancestry" },
761 { "value" => "1000GENOMES:phase_3:CHB", "caption" => "Han Chinese in Bejing, China" },
762 { "value" => "1000GENOMES:phase_3:CHS", "caption" => "Southern Han Chinese, China" },
763 { "value" => "1000GENOMES:phase_3:CLM", "caption" => "Colombian in Medellin, Colombia" },
764 { "value" => "1000GENOMES:phase_3:ESN", "caption" => "Esan in Nigeria" },
765 { "value" => "1000GENOMES:phase_3:FIN", "caption" => "Finnish in Finland" },
766 { "value" => "1000GENOMES:phase_3:GBR", "caption" => "British in England and Scotland" },
767 { "value" => "1000GENOMES:phase_3:GIH", "caption" => "Gujarati Indian in Houston, TX" },
768 { "value" => "1000GENOMES:phase_3:IBS", "caption" => "Iberian populations in Spain" },
769 { "value" => "1000GENOMES:phase_3:ITU", "caption" => "Indian Telugu in the UK" },
770 { "value" => "1000GENOMES:phase_3:JPT", "caption" => "Japanese in Tokyo, Japan" },
771 { "value" => "1000GENOMES:phase_3:KHV", "caption" => "Kinh in Ho Chi Minh City, Vietnam" },
772 { "value" => "1000GENOMES:phase_3:LWK", "caption" => "Luhya in Webuye, Kenya" },
773 { "value" => "1000GENOMES:phase_3:MAG", "caption" => "Mandinka in The Gambia" },
774 { "value" => "1000GENOMES:phase_3:MSL", "caption" => "Mende in Sierra Leone" },
775 { "value" => "1000GENOMES:phase_3:MXL", "caption" => "Mexican Ancestry in Los Angeles, California" },
776 { "value" => "1000GENOMES:phase_3:PEL", "caption" => "Peruvian in Lima, Peru" },
777 { "value" => "1000GENOMES:phase_3:PJL", "caption" => "Punjabi in Lahore, Pakistan" },
778 { "value" => "1000GENOMES:phase_3:PUR", "caption" => "Puerto Rican in Puerto Rico" },
779 { "value" => "1000GENOMES:phase_3:STU", "caption" => "Sri Lankan Tamil in the UK" },
780 { "value" => "1000GENOMES:phase_3:TSI", "caption" => "Toscani in Italy" },
781 { "value" => "1000GENOMES:phase_3:YRI", "caption" => "Yoruba in Ibadan, Nigeria" },
782 ],
783 "value" => "1000GENOMES:phase_3:CEU",
784 },
785 {
786 "name" => "threshold",
787 "label" => "r2 cutoff",
788 "type" => "string",
789 "value" => 0.8,
790 },
791 ]
792 },
793
794 # SameCodon
795 {
796 "key" => "SameCodon",
797 "label" => "Variants in same codon",
798 "helptip" => "Reports existing variants that fall in the same codon",
799 "available" => 0,
800 "enabled" => 0,
801 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/SameCodon.pm",
802 "section" => "Variant data",
803 },
804 # LOVD
805 {
806 "key" => "LOVD",
807 "label" => "LOVD",
808 "helptip" => "Retrieves LOVD variation data",
809 "available" => 0,
810 "enabled" => 0,
811 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LOVD.pm",
812 "section" => "Variant data",
813 },
814
815 # GO
816 {
817 "key" => "GO",
818 "label" => "Gene Ontology",
819 "helptip" => "Retrieves Gene Ontology terms associated with transcripts/translations via the Ensembl API",
820 "available" => 0,
821 "enabled" => 0,
822 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/GO.pm",
823 "section" => "Gene data",
824 },
825
826 # Downstream
827 {
828 "key" => "Downstream",
829 "label" => "Downstream",
830 "helptip" => "Predicts the downstream effects of a frameshift variant on the protein sequence of a transcript",
831 "available" => 0,
832 "enabled" => 0,
833 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Downstream.pm",
834 },
835
836 # ProteinSeqs
837 {
838 "key" => "ProteinSeqs",
839 "label" => "Protein sequences",
840 "helptip" => "Prints out the reference and mutated protein sequences of any proteins found with non-synonymous mutations",
841 "available" => 0,
842 "enabled" => 0,
843 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/ProteinSeqs.pm",
844 },
845
846 # TSSDistance
847 {
848 "key" => "TSSDistance",
849 "label" => "TSS distance",
850 "helptip" => "Calculates the distance from the transcription start site for upstream variants ",
851 "available" => 0,
852 "enabled" => 0,
853 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/TSSDistance.pm",
854 },
855
856 # Phenotypes
857 {
858 "key" => "Phenotypes",
859 "label" => "Phenotypes",
860 "helptip" => "Retrieves overlapping phenotype annotations",
861 "available" => 0,
862 "enabled" => 0,
863 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Phenotypes.pm",
864 },
865 # Draw
866 {
867 "key" => "Draw",
868 "label" => "Draw",
869 "helptip" => "Creates images of the transcript model showing variant location",
870 "available" => 0,
871 "enabled" => 0,
872 "requires_install" => 1,
873 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Draw.pm",
874 },
875 # G2P
876 {
877 "key" => "G2P",
878 "label" => "G2P",
879 "helptip" => "Assesses variants using G2P allelic requirements for potential phenotype involvement.",
880 "available" => 0,
881 "enabled" => 0,
882 "requires_data" => 1,
883 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/G2P.pm",
884 },
885
886 # LocalID
887 {
888 "key" => "LocalID",
889 "label" => "LocalID",
890 "helptip" => "Allows you to use variant IDs as VEP input without making a database connection.",
891 "available" => 0,
892 "enabled" => 0,
893 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LocalID.pm",
894 },
895
896
897 ]
898 };