Mercurial > repos > dereeper > snpeff_from_gff_vcf

view snpEff-pipe.sh @ 0:abde5b0387c8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Mon, 23 Mar 2015 05:17:19 -0400
parents
children
line wrap: on
line source

#!/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