Mercurial > repos > dereeper > snpeff_from_gff_vcf

diff snpEff-pipe.sh @ 0:abde5b0387c8 draft

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author dereeper
date Mon, 23 Mar 2015 05:17:19 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff-pipe.sh	Mon Mar 23 05:17:19 2015 -0400
@@ -0,0 +1,14 @@
+#!/bin/bash
+vcf=$1
+genome=$2
+gff=$3
+output=$4
+html=$5
+log=$6
+
+directory=`dirname $0`
+ 
+/usr/bin/perl $directory/SnpEff.pl -i $vcf -f $genome -g $gff -o $output -h $html >>$log 2>&1
+
+
+