Mercurial > repos > dereeper > snpeff_from_gff_vcf

comparison 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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-1:000000000000 0:abde5b0387c8
1 #!/bin/bash
2 vcf=$1
3 genome=$2
4 gff=$3
5 output=$4
6 html=$5
7 log=$6
8
9 directory=`dirname $0`
10
11 /usr/bin/perl $directory/SnpEff.pl -i $vcf -f $genome -g $gff -o $output -h $html >>$log 2>&1
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