| Next changeset 1:f49b23b41a12 (2015-11-11) |
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Commit message:
Uploaded |
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added:
macros.xml test-data/vcfallelicprimitives-test1.vcf test-data/vcflib.vcf tool_dependencies.xml vcfallelicprimitives.xml |
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| diff -r 000000000000 -r 3f4fefbc52c8 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 19 12:23:24 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 3f4fefbc52c8 test-data/vcfallelicprimitives-test1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfallelicprimitives-test1.vcf Thu Mar 19 12:23:24 2015 -0400 |
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| @@ -0,0 +1,35 @@ +##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=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=Split primitives,Number=0,Type=Flag,Description="The allele was parsed using vcfallelicprimitives."> +#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 AF=0.5;DP=14;NS=3;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 AF=0.017;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 . A G,T 67 PASS AF=0.333,0.667;LEN=1,1;TYPE=snp,snp;Split primitives GT 1|2 2|1 2|2 +20 1230237 . T . 47 PASS AA=T;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 . G GA,GAC 50 PASS AC=3,1;LEN=1,2;TYPE=ins,ins;Split primitives GT 0|1 0|2 1|1 +20 1235237 . T . 0 . . GT 0/0 0|0 . +X 10 . AC ATC,A 10 PASS LEN=1,1;TYPE=ins,del;Split primitives GT 0 0|2 0|1 +X 11 . C G 10 PASS LEN=1;TYPE=snp;Split primitives GT 0 0|0 0|1 |
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| diff -r 000000000000 -r 3f4fefbc52c8 test-data/vcflib.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcflib.vcf Thu Mar 19 12:23:24 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 3f4fefbc52c8 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Mar 19 12:23:24 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 3f4fefbc52c8 vcfallelicprimitives.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfallelicprimitives.xml Thu Mar 19 12:23:24 2015 -0400 |
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| @@ -0,0 +1,62 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.3"> + <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio" /> + <command> + cat "${input}" | vcfallelicprimitives + ${m_option} + -t "${t_option}" + -L "${max_length}" + $keep_info + $keep_geno > "${out_file1}" + </command> + <inputs> + <param format="vcf" name="input" type="data" label="Select VCF dataset"/> + <param name="m_option" type="boolean" checked="false" truevalue="--use-mnps" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/> + <param name="t_option" size="20" type="text" value="Split primitives" label="Tag records which are split apart of a complex allele with this flag. " help="--tag-parsed option"/> + <param name="max_length" type="integer" size="4" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/> + <param name="keep_info" type="boolean" truevalue="--keep-info" falsevalue="" checked="False" + label="Maintain site and allele-level annotations when decomposing" + help="Note that in many cases, such as multisample VCFs, these won't be valid post-decomposition. For biallelic loci in single-sample VCFs, they should be usable with caution. (--keep-info)"/> + <param name="keep_geno" type="boolean" truevalue="--keep-geno" falsevalue="" checked="False" + label="Maintain genotype-level annotations when decomposing" + help="Similar caution should be used for this as for --keep-info. (--keep-geno)"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfallelicprimitives-test1.vcf"/> + </test> + </tests> + <help> + +If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, this tools splits the record into multiple lines, but drops all INFO fields. +"Pure" MNPs are split into multiple SNPs unless the -m flag is provided. +Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input. + +The options are:: + + -m, --use-mnps Retain MNPs as separate events (default: false). + -t, --tag-parsed FLAG Tag records which are split apart of a complex allele with this flag. + -L, --max-length LEN Do not manipulate records in which either the ALT or + REF is longer than LEN (default: 200). + -k, --keep-info Maintain site and allele-level annotations when decomposing. + Note that in many cases, such as multisample VCFs, these won't + be valid post-decomposition. For biallelic loci in single-sample + VCFs, they should be usable with caution. + -g, --keep-geno Maintain genotype-level annotations when decomposing. Similar + caution should be used for this as for --keep-info. + +---- + +Vcfallelicprimitives @IS_PART_OF_VCFLIB@ + </help> + <expand macro="citations" /> +</tool> |