| Next changeset 1:834e1f313036 (2015-11-11) |
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Commit message:
Uploaded |
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added:
macros.xml test-data/vcfannotate.bed test-data/vcfbedintersect-test1.vcf test-data/vcfbedintersect-test2.vcf test-data/vcflib.vcf tool_dependencies.xml vcfbedintersect.xml |
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| diff -r 000000000000 -r 8a482a9aa45d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 19 12:42:11 2015 -0400 |
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| @@ -0,0 +1,28 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="8a5602bf07">vcflib</requirement> + <yield/> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> +@misc{Garrison2015, + author = {Garrison, Erik}, + year = {2015}, + title = {vcflib}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ekg/vcflib}, +} + </citation> + </citations> + </xml> + <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token> +</macros> |
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| diff -r 000000000000 -r 8a482a9aa45d test-data/vcfannotate.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfannotate.bed Thu Mar 19 12:42:11 2015 -0400 |
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| @@ -0,0 +1,46 @@ +20 123251 126392 uc002wcx.3 0 + 123269 126333 0 2 76,337, 0,2804, +20 138110 139804 uc002wcy.2 0 + 138185 139665 0 2 124,390, 0,1304, +20 168526 170264 uc002wcz.1 0 - 168526 170264 0 2 233,49, 0,1689, +20 207898 210527 uc002wda.3 0 + 207929 210412 0 2 89,609, 0,2020, +20 238376 241736 uc002wdb.3 0 + 238419 239947 0 2 101,2019, 0,1341, +20 251503 271419 uc021vzl.1 0 - 251847 271244 0 11 405,119,87,102,158,100,159,119,118,49,192, 0,5105,5930,6181,6363,7467,8309,13100,18696,19396,19724, +20 251503 271419 uc002wde.2 0 - 251847 271251 0 11 405,119,87,102,158,100,159,119,118,49,188, 0,5105,5930,6181,6363,7467,8309,13100,18696,19396,19728, +20 251503 271419 uc010zpi.2 0 - 251847 270227 0 10 405,119,87,102,158,100,159,119,118,188, 0,5105,5930,6181,6363,7467,8309,13100,18696,19728, +20 256608 271079 uc010zpj.1 0 - 257400 270981 0 7 912,102,158,100,159,119,180, 0,1076,1258,2362,3204,7995,14291, +20 256608 271419 uc010zpk.2 0 - 257400 271232 0 7 912,102,158,100,159,119,188, 0,1076,1258,2362,3204,7995,14623, +20 278203 280963 uc002wdf.3 0 + 278227 279442 0 1 2760, 0, +20 306214 310872 uc002wdh.4 0 + 306568 307516 0 1 4658, 0, +20 327369 335512 uc002wdi.4 0 + 330287 334279 0 4 417,115,195,1659, 0,2523,2912,6484, +20 361307 378203 uc002wdm.3 0 + 368654 377334 0 4 506,291,293,1362, 0,7347,10623,15534, +20 361940 378203 uc002wdn.3 0 + 363189 377334 0 5 204,194,291,293,1362, 0,1136,6714,9990,14901, +20 388708 391408 uc002wdo.3 0 + 388708 388708 0 3 715,145,353, 0,1816,2347, +20 388708 400504 uc010zpl.1 0 + 389401 400429 0 6 715,145,94,199,122,303, 0,1816,9461,9667,11282,11493, +20 388708 409233 uc010zpm.1 0 + 388708 388708 0 9 715,145,94,199,122,174,112,180,99, 0,1816,9461,9667,11282,11493,14062,19248,20426, +20 388708 411610 uc002wdp.4 0 + 389401 411074 0 12 715,145,94,199,122,174,161,112,180,99,144,617, 0,1816,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc002wdq.4 0 + 389382 411074 0 11 715,94,199,122,174,161,112,180,99,144,617, 0,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc010fzy.3 0 + 388708 388708 0 12 715,145,94,199,122,174,136,112,180,99,144,617, 0,1816,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc002wdr.4 0 + 398463 411074 0 10 715,94,199,122,174,112,180,99,144,617, 0,9461,9667,11282,11493,14062,19248,20426,20886,22285, +20 416123 443187 uc002wds.3 0 - 419229 443049 0 8 3362,188,142,102,187,81,186,208, 0,3628,4768,6108,6377,9570,12409,26856, +20 416123 443187 uc002wdt.3 0 - 416123 416123 0 10 491,159,292,188,142,102,187,81,186,208, 0,1960,3070,3628,4768,6108,6377,9570,12409,26856, +20 416123 443187 uc002wdv.3 0 - 419229 422326 0 7 3362,188,142,456,81,186,208, 0,3628,4768,6108,9570,12409,26856, +20 416125 417600 uc021vzm.1 0 - 416125 416125 0 1 1475, 0, +20 463337 524482 uc002wdw.1 0 - 464604 489195 0 14 1383,87,149,101,102,111,84,60,51,102,112,210,117,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,25757,45239,60978, +20 463337 524482 uc002wdx.1 0 - 464604 489195 0 13 1383,87,149,101,102,111,84,60,51,102,112,210,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,25757,60978, +20 463337 524482 uc002wdy.1 0 - 464604 478382 0 12 1383,87,149,101,102,111,84,60,51,102,112,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,60978, +20 584636 590910 uc002wdz.3 0 - 585234 590881 0 2 673,554, 0,5720, +20 627267 634014 uc002wea.4 0 - 629357 633829 0 2 2294,395, 0,6352, +20 627267 656823 uc002web.4 0 - 629499 656245 0 3 2294,90,711, 0,7607,28845, +20 642239 656823 uc002wec.3 0 - 644314 656245 0 2 2866,711, 0,13873, +20 740723 749228 uc002wed.4 0 - 741669 746418 0 5 1159,124,506,618,288, 0,1621,3418,5128,8217, +20 740724 749228 uc002wee.2 0 - 742293 746418 0 4 1744,506,618,288, 0,3417,5127,8216, +20 814355 826922 uc002wef.1 0 + 825447 826335 0 2 239,1572, 0,10995, +20 816710 826922 uc002weg.1 0 + 825447 826335 0 2 47,1572, 0,8640, +20 825284 826922 uc002weh.1 0 + 825447 826335 0 1 1638, 0, +20 853296 896960 uc002wei.3 0 - 853602 896857 0 9 467,131,167,102,116,248,122,156,412, 0,1630,5507,7093,8517,12424,15664,17559,43252, +20 853296 896960 uc010zpn.2 0 - 853750 896839 0 8 467,167,102,116,248,122,156,412, 0,5507,7093,8517,12424,15664,17559,43252, +20 939095 982907 uc002wej.3 0 - 940999 982807 0 5 2014,186,141,189,179, 0,5482,8721,9497,43633, +20 939095 982907 uc002wek.3 0 - 940999 982807 0 4 2014,141,189,179, 0,8721,9497,43633, +20 1093905 1147970 uc010zpo.2 0 + 1106275 1146898 0 7 147,153,83,186,54,159,1100, 0,12235,14163,21858,49868,51056,52965, +20 1093905 1148426 uc002wel.4 0 + 1099416 1145724 0 8 147,150,153,83,186,54,159,2754, 0,5490,12235,14163,21858,49868,51056,51767, +20 1099239 1147970 uc010zpp.2 0 + 1099416 1146898 0 6 306,153,83,54,159,1100, 0,6901,8829,44534,45722,47631, +20 1099239 1148426 uc002wen.4 0 + 1099416 1145724 0 7 306,153,83,186,54,159,2754, 0,6901,8829,16524,44534,45722,46433, |
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| diff -r 000000000000 -r 8a482a9aa45d test-data/vcfbedintersect-test1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfbedintersect-test1.vcf Thu Mar 19 12:42:11 2015 -0400 |
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| @@ -0,0 +1,23 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> +##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> +##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> +##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> +##FILTER=<ID=q10,Description="Quality below 10"> +##FILTER=<ID=s50,Description="Less than 50% of samples have data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> +##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> +##ALT=<ID=CNV,Description="Copy number variable region"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. |
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| diff -r 000000000000 -r 8a482a9aa45d test-data/vcfbedintersect-test2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfbedintersect-test2.vcf Thu Mar 19 12:42:11 2015 -0400 |
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| @@ -0,0 +1,24 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> +##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> +##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> +##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> +##FILTER=<ID=q10,Description="Quality below 10"> +##FILTER=<ID=s50,Description="Less than 50% of samples have data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> +##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> +##ALT=<ID=CNV,Description="Copy number variable region"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. |
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| diff -r 000000000000 -r 8a482a9aa45d test-data/vcflib.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcflib.vcf Thu Mar 19 12:42:11 2015 -0400 |
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| @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> +##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> +##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> +##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> +##FILTER=<ID=q10,Description="Quality below 10"> +##FILTER=<ID=s50,Description="Less than 50% of samples have data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> +##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> +##ALT=<ID=CNV,Description="Copy number variable region"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 |
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| diff -r 000000000000 -r 8a482a9aa45d tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Mar 19 12:42:11 2015 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="vcflib" version="8a5602bf07"> + <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
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| diff -r 000000000000 -r 8a482a9aa45d vcfbedintersect.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfbedintersect.xml Thu Mar 19 12:42:11 2015 -0400 |
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| @@ -0,0 +1,62 @@ +<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.3"> + <description>Intersect VCF and BED datasets</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio" /> + <command> + #if str($bed_vs_interval.bed_vs_interval_selector) == "bed": + vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}" + #else: + vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}" + #end if + + </command> + <inputs> + <!-- selecting refernce source --> + <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" /> + <conditional name="bed_vs_interval"> + <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with"> + <option value="bed">BED</option> + <option value="interval">Interval</option> + </param> + <when value="bed"> + <param name="bed_input" type="data" format="bed" label="Select BED dataset" /> + </when> + <when value="interval"> + <param name="int_input" type="text" size="20" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" /> + </when> + </conditional> + <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." /> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="bed_vs_interval_selector" value="bed" /> + <param name="bed_input" value="vcfannotate.bed" /> + <param name="invert" value="False" /> + <param name="vcf_input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfbedintersect-test1.vcf"/> + </test> + <test> + <param name="bed_vs_interval_selector" value="interval" /> + <param name="int_input" value="20:1-30000" /> + <param name="invert" value="False" /> + <param name="vcf_input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfbedintersect-test2.vcf"/> + </test> + </tests> + + <help> + +Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end). + +---- + +VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). +</help> + <expand macro="citations" /> +</tool> |