Mercurial > repos > gandres > vcftools_filter_stats_diversity

diff vcftools_main/VCFToolsStats/vcfToolsStats.sh @ 0:3b1436a9a6e5 draft

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author gandres
date Thu, 02 Jul 2015 05:21:40 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcftools_main/VCFToolsStats/vcfToolsStats.sh	Thu Jul 02 05:21:40 2015 -0400
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+tool_path=$(dirname $0)
+
+filein=$1
+fileout_label=$2
+fileout_annot=$3
+fileout_het=$4
+fileout_imiss=$5
+fileout_sum=$6
+filelog=$7
+
+
+
+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