Mercurial > repos > a.gkanogiannis > prune_ld
changeset 0:10ead977a5cf draft default tip
Uploaded
| author | a.gkanogiannis |
|---|---|
| date | Tue, 06 Feb 2018 04:13:04 -0500 |
| parents | |
| children | |
| files | plink_ld_prune.sh plink_ld_prune.xml |
| diffstat | 2 files changed, 47 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plink_ld_prune.sh Tue Feb 06 04:13:04 2018 -0500 @@ -0,0 +1,9 @@ +#!/bin/bash + +# usage : sh plink_ld_prune.sh <input VCF file> <output file prefix> <window size in snps or add kb> <step size> <r^2 threshold> + +plink=$(compgen -c plink) +plink=$(which $plink) + +$plink --vcf $1 --allow-extra-chr --out $2 --indep-pairwise $3 $4 $5 && +$plink --vcf $1 --allow-extra-chr --recode vcf --extract $2.prune.in --out $2.pruned
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plink_ld_prune.xml Tue Feb 06 04:13:04 2018 -0500 @@ -0,0 +1,38 @@ +<tool id="plink_ld_prune" name="Prune SNPs" version="0.1.0"> + <description>on LD threshold (plink)</description> + <requirements> + <requirement type="package" version="1.9">plink</requirement> + </requirements> + + <command interpreter="bash"><![CDATA[ + plink_ld_prune.sh "${par1}" "output" "${par3}" "${par4}" "${par5}" && + cp "output.pruned.vcf" "${output}" + ]]></command> + + + <inputs> + <param format="vcf" name="par1" type="data" label="Input VCF file"/> + <param name="par3" type="text" label="window size in snps or add kb"/> + <param name="par4" type="text" label="step size"/> + <param name="par5" type="text" label="r^2 threshold"/> + </inputs> + + <outputs> + <data format="vcf" name="output" /> + </outputs> + + <tests> + <test> + <param name="par1" value="input.vcf"/> + <param name="par3" value="1000kb"/> + <param name="par4" value="5"/> + <param name="par5" value="0.25"/> + <output name="output" file="output.pruned.vcf"/> + </test> + </tests> + + <help> + Prune SNPs on LD threshold (plink) + </help> + +</tool>