Mercurial > repos > ulfschaefer > phephenix

comparison filter_vcf.sh @ 5:e2ee6acf8752 draft

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Uploaded
author ulfschaefer
date Thu, 16 Jun 2016 06:39:37 -0400
parents cb29f95c7b88
children
comparison
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4:7ccbcc8608fa 5:e2ee6acf8752
4 4
5 OUTPUT=$1 5 OUTPUT=$1
6 shift 6 shift
7 VCF=$1 7 VCF=$1
8 shift 8 shift
9 REF=$1
10 shift
9 ONLYGOOD=$1 11 ONLYGOOD=$1
10 shift 12 shift
11 FILTERS=$@ 13 FILTERS=$@
12 14
13 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') 15 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
14 16
15 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT" 17 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT --reference $REF"
16 18
17 if [ $ONLYGOOD != "NOTTHERE" ]; then 19 if [ $ONLYGOOD != "NOTTHERE" ]; then
18 CMD="$CMD --only-good" 20 CMD="$CMD --only-good"
19 fi 21 fi
20 22