Mercurial > repos > ulfschaefer > phe_phenix

comparison filter_vcf.sh @ 0:99ff94f3d11f draft

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author ulfschaefer
date Tue, 19 Apr 2016 11:59:39 -0400
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-1:000000000000 0:99ff94f3d11f
1 #!/bin/bash
2
3 echo $@
4
5 OUTPUT=$1
6 shift
7 VCF=$1
8 shift
9 FILTERS=$@
10
11 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
12
13 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT"
14
15 echo "CMD: "$CMD
16 eval $CMD