Mercurial > repos > gandres > vcftools_filter_stats_diversity
view VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh @ 3:612066e3f57d draft
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author | gandres |
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date | Mon, 09 Nov 2015 05:18:45 -0500 |
parents | |
children | b762ecbe2314 |
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#!/bin/bash tool_path=$(dirname $0) filein=$1 fileout_label=$(date "+%Y%m%d%H%M%S") step=$2 window=$3 filelog=$4 fileout_taj=$5 fileout_tstv=$6 fileout_windowed=$7 fileout_snp=$8 group=$9 if [ "$group" != "none" ] then fileout_fst=${10} fileout_fst_marker=${11} fileout_taj_combined=${12} fileout_windowed_combined=${13} fi cp $filein ${filein}.vcf if [ "$group" != "none" ] then perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --step $step --window $window --group $group else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --step $step --window $window fi mv ${fileout_label}.vcftools.log $filelog mv ${fileout_label}.Tajima.D ${fileout_taj} mv ${fileout_label}.TsTv ${fileout_tstv} mv ${fileout_label}.windowed.pi ${fileout_windowed} mv ${fileout_label}.snpden ${fileout_snp} if [ "$group" != "none" ] then mv ${fileout_label}.fst.txt ${fileout_fst} mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker} mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined} mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined} fi rm -f ${filein}.vcf ${filein}.vcf.*