Mercurial > repos > dereeper > snpeff_from_gff_vcf

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