# HG changeset patch # User devteam # Date 1447090386 18000 # Node ID 1de250ea8c1a3cbd815585f83a91e1643bb2ffe5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b diff -r 000000000000 -r 1de250ea8c1a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Nov 09 12:33:06 2015 -0500 @@ -0,0 +1,28 @@ + + + + vcflib + + + + + + + + + + + +@misc{Garrison2015, + author = {Garrison, Erik}, + year = {2015}, + title = {vcflib}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ekg/vcflib}, +} + + + + is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + diff -r 000000000000 -r 1de250ea8c1a test-data/vcfhethom-test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfhethom-test1.tab Mon Nov 09 12:33:06 2015 -0500 @@ -0,0 +1,2 @@ +NA00001 NA00002 NA00003 +1 4 3 diff -r 000000000000 -r 1de250ea8c1a test-data/vcfhethom-test2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfhethom-test2.tab Mon Nov 09 12:33:06 2015 -0500 @@ -0,0 +1,2 @@ +NA00001 NA00002 NA00003 +inf inf 1 diff -r 000000000000 -r 1de250ea8c1a test-data/vcfhethom-test3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfhethom-test3.tab Mon Nov 09 12:33:06 2015 -0500 @@ -0,0 +1,1 @@ +21 diff -r 000000000000 -r 1de250ea8c1a test-data/vcflib.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcflib.vcf Mon Nov 09 12:33:06 2015 -0500 @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#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 diff -r 000000000000 -r 1de250ea8c1a tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Nov 09 12:33:06 2015 -0500 @@ -0,0 +1,6 @@ + + + + + + diff -r 000000000000 -r 1de250ea8c1a vcfhethom.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfhethom.xml Mon Nov 09 12:33:06 2015 -0500 @@ -0,0 +1,62 @@ + + Count the number of heterozygotes and alleles, compute het/hom ratio + + macros.xml + + + + + + #if str($analysis_type) == "count": + vcfhetcount "${vcf_input}" > "${out_file1}" + #elif str($analysis_type) == "ratio": + vcfhethomratio "${vcf_input}" > "${out_file1}" + #elif str($analysis_type) == "allele_count": + vcfcountalleles "${vcf_input}" > "${out_file1}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +This tool performs three basic calculations: + +(1) Computes the number of heterozygotes +(2) Computes the ratio between heterozygotes and homozygotes +(3) Computes the total number of alleles in the input dataset + +---- + +This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + + + +