Mercurial > repos > ulfschaefer > phe_phenix

diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_vcf.sh	Tue Apr 19 11:59:39 2016 -0400
@@ -0,0 +1,16 @@
+#!/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