Mercurial > repos > anton > vcfannotategenotypes
annotate vcfannotategenotypes.xml @ 1:7d46a899f2a5
Updated to vcflib 86723982aa
| author | Anton Nekrutenko <anton@bx.psu.edu> |
|---|---|
| date | Wed, 25 Jun 2014 16:20:11 -0400 |
| parents | 346257ed6413 |
| children | 846a4449a50a |
| rev | line source |
|---|---|
| 0 | 1 <tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.1"> |
| 2 <requirements> | |
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7d46a899f2a5
Updated to vcflib 86723982aa
Anton Nekrutenko <anton@bx.psu.edu>
parents:
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changeset
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3 <requirement type="package" version="86723982aa">vcflib</requirement> |
| 0 | 4 </requirements> |
| 5 <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description> | |
| 6 <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command> | |
| 7 <inputs> | |
| 8 <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/> | |
| 9 <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/> | |
| 10 <param name="tag_option" size="20" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data format="vcf" name="out_file1" /> | |
| 14 </outputs> | |
| 15 <tests> | |
| 16 <test> | |
| 17 <param name="tag_option" value="added-genotypes"/> | |
| 18 <param name="input1" value="vcflib.vcf"/> | |
| 19 <param name="input2" value="vcfannotategenotypes-input2.vcf"/> | |
| 20 <output name="out_file1" file="vcfannotategenotypes-test1.vcf" /> | |
| 21 </test> | |
| 22 </tests> | |
| 23 <help> | |
| 24 | |
| 25 Annotates genotypes in the **First** file with genotypes in the **Second** adding the genotype as another flag to each sample filed in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation. also adds a 'has\_variant' flag for sites where the second file has a variant. | |
| 26 | |
| 27 ----- | |
| 28 | |
| 29 Vcfannotate is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 30 | |
| 31 | |
| 32 </help> | |
| 33 </tool> |