Mercurial > repos > anton > vcfannotate
annotate vcfannotate.xml @ 3:28459b837ef8 draft default tip
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| author | anton |
|---|---|
| date | Mon, 15 Sep 2014 14:48:28 -0400 |
| parents | 98961914308d |
| children |
| rev | line source |
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98961914308d
Updated tool version to 0.0.2
Anton Nekrutenko <anton@bx.psu.edu>
parents:
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changeset
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1 <tool id="vcfannotate" name="VCFannotate:" version="0.0.2"> |
| 0 | 2 <requirements> |
| 3 | 3 <requirement type="package" version="8a5602bf07">vcflib</requirement> |
| 0 | 4 </requirements> |
| 5 <description>Intersect VCF records with BED annotations</description> | |
| 6 <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command> | |
| 7 <inputs> | |
| 8 <param format="vcf" name="input" type="data" label="Select VCF dataset"/> | |
| 3 | 9 <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/> |
| 0 | 10 <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"/> |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data format="vcf" name="out_file1" /> | |
| 14 </outputs> | |
| 15 <tests> | |
| 16 <test> | |
| 17 <param name="bed_data" value="vcfannotate.bed" ftype="bed"/> | |
| 18 <param name="key_option" value="BED-features"/> | |
| 19 <param name="input" value="vcflib.vcf"/> | |
| 20 <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" /> | |
| 21 </test> | |
| 22 </tests> | |
| 23 <help> | |
| 24 | |
| 3 | 25 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. |
| 0 | 26 |
| 27 ----- | |
| 28 | |
| 29 .. class:: infomark | |
| 30 | |
| 31 | |
| 32 **Example**: | |
| 33 | |
| 34 The following VCF line:: | |
| 35 | |
| 36 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 | |
| 37 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:.,. | |
| 38 | |
| 39 will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen:: | |
| 40 | |
| 41 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 | |
| 42 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:.,. | |
| 43 | |
| 44 ---- | |
| 45 | |
| 46 Vcfannotate is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 47 | |
| 48 | |
| 49 </help> | |
| 50 </tool> |