Mercurial > repos > anton > vcfannotate
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author | anton |
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date | Mon, 15 Sep 2014 14:48:28 -0400 |
parents | 98961914308d |
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<tool id="vcfannotate" name="VCFannotate:" version="0.0.2"> <requirements> <requirement type="package" version="8a5602bf07">vcflib</requirement> </requirements> <description>Intersect VCF records with BED annotations</description> <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command> <inputs> <param format="vcf" name="input" type="data" label="Select VCF dataset"/> <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/> <param name="key_option" size="20" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/> </inputs> <outputs> <data format="vcf" name="out_file1" /> </outputs> <tests> <test> <param name="bed_data" value="vcfannotate.bed" ftype="bed"/> <param name="key_option" value="BED-features"/> <param name="input" value="vcflib.vcf"/> <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" /> </test> </tests> <help> Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file. ----- .. class:: infomark **Example**: The following VCF line:: #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:.,. will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen:: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;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:.,. ---- Vcfannotate is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). </help> </tool>