Mercurial > repos > anton > vcfannotate
annotate vcfannotate.xml @ 1:044448c58323
Updated to vcflib 86723982aa
author | Anton Nekrutenko <anton@bx.psu.edu> |
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date | Wed, 25 Jun 2014 16:01:27 -0400 |
parents | 027fe0a0076e |
children | 98961914308d |
rev | line source |
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0 | 1 <tool id="vcfannotate" name="VCFannotate:" version="0.0.1"> |
2 <requirements> | |
1
044448c58323
Updated to vcflib 86723982aa
Anton Nekrutenko <anton@bx.psu.edu>
parents:
0
diff
changeset
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3 <requirement type="package" version="86723982aa">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"/> | |
9 <param name="bed_data" type="data" format="bed" label="BED datasets to itersect with"/> | |
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 | |
25 Intersect the records in the VCF file with targets provided in a BED file. Intersections are done on the reference sequences in the VCF file. | |
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> |