| Next changeset 1:ff5c6635c9a8 (2014-06-25) |
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Commit message:
Imported from capsule None |
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added:
test-data/vcfdistance-test1.vcf test-data/vcflib.vcf tool_dependencies.xml vcfdistance.xml |
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| diff -r 000000000000 -r de3bbf60d086 test-data/vcfdistance-test1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfdistance-test1.vcf Wed Jun 11 17:11:17 2014 -0400 |
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| @@ -0,0 +1,29 @@ +##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"> +##INFO=<ID=BasesToClosestVariant,Number=1,Type=Integer,Description="Number of bases to the closest variant in the file."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . BasesToClosestVariant=1 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . BasesToClosestVariant=1 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 17330 . T A 3 q10 AF=0.017;BasesToClosestVariant=1093366;DP=11;NS=3 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 AA=T;AF=0.333,0.667;BasesToClosestVariant=119541;DP=10;NS=2;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 AA=T;BasesToClosestVariant=4330;DP=13;NS=3 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 AA=G;AC=3,1;AN=6;BasesToClosestVariant=670;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 |
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| diff -r 000000000000 -r de3bbf60d086 test-data/vcflib.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcflib.vcf Wed Jun 11 17:11:17 2014 -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 de3bbf60d086 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jun 11 17:11:17 2014 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="vcflib" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd"> + <repository changeset_revision="7949cc09120a" name="package_vcflib" owner="anton" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
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| diff -r 000000000000 -r de3bbf60d086 vcfdistance.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfdistance.xml Wed Jun 11 17:11:17 2014 -0400 |
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| @@ -0,0 +1,32 @@ +<tool id="vcfdistance" name="VCFdistance:" version="0.0.1"> +<requirements> + <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> +</requirements> + <description>Calculate distance to the nearest variant</description> + <command>cat "${input1}" | vcfdistance > "${out_file1}"</command> + <inputs> + <param format="vcf" name="input1" type="data" label="First dataset"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcfdistance-test1.vcf"/> + </test> + </tests> + <help> + +Adds a value to each VCF record indicating the distance to the nearest variant in the file. + +.. class:: infomark + +The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). + +---- + +Vcfdistance is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + +</help> +</tool> |