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view filter_vcf.sh @ 5:1f1ec89759d4 draft

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author ulfschaefer
date Fri, 22 Apr 2016 09:45:31 -0400
parents 45ff0fc972e8
children a6079f6217f5
line wrap: on
line source

#!/bin/bash

echo $@

OUTPUT=$1
shift
VCF=$1
shift
FILTERS=$@

FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')

CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT"

echo "CMD: "$CMD
eval $CMD