Mercurial > repos > ulfschaefer > phephenix
view filter_vcf.sh @ 2:79fc19ba1cbc draft
Uploaded
author | ulfschaefer |
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date | Tue, 10 May 2016 09:02:04 -0400 |
parents | cb29f95c7b88 |
children | e2ee6acf8752 |
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#!/bin/bash # echo $@ OUTPUT=$1 shift VCF=$1 shift ONLYGOOD=$1 shift FILTERS=$@ FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT" if [ $ONLYGOOD != "NOTTHERE" ]; then CMD="$CMD --only-good" fi echo "CMD: "$CMD eval $CMD