Mercurial > repos > ulfschaefer > filter_vcf

comparison filter_vcf.sh @ 4:5dfc843979c2 draft

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author ulfschaefer
date Fri, 11 Dec 2015 10:07:49 -0500
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3:879d0f13a737 4:5dfc843979c2
1 #!/bin/bash
2
3 OUTPUT=$1
4 shift
5 VCF=$1
6 shift
7 FILTERS=$@
8
9 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
10 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
11 export PATH=$PATH:$DIR
12 CMD="filter_vcf.py --vcf $VCF --filters $FILTERS --output $OUTPUT"
13
14 echo "CMD: "$CMD
15 eval $CMD