Mercurial > repos > gandres > vcftools_filter_stats_diversity

view VCFToolsStats/vcfToolsStats.sh @ 4:b762ecbe2314 draft

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planemo upload
author gandres
date Fri, 11 Dec 2015 07:35:00 -0500
parents 612066e3f57d
children 2b6bb9d5e4e9
line wrap: on
line source

#!/bin/bash

tool_path=$(dirname $0)

filein=$1
fileout_label=$(date "+%Y%m%d%H%M%S")
fileout_annot=$2
fileout_het=$3
fileout_imiss=$4
fileout_sum=$5
filelog=$6



perl $tool_path/VCFToolsStats.pl --input $filein --out $fileout_label

cp  $fileout_label.annotation $fileout_annot ; rm $fileout_label.annotation
cp  $fileout_label.het $fileout_het ; rm $fileout_label.het
cp  $fileout_label.imiss $fileout_imiss ; rm $fileout_label.imiss
cp  $fileout_label.TsTv.summary $fileout_sum ; rm $fileout_label.TsTv.summary

cp vcftools.log $filelog
rm vcftools.log