Mercurial > repos > ulfschaefer > filter_vcf

diff filter_vcf.sh @ 0:834a312c0114 draft

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author ulfschaefer
date Thu, 10 Dec 2015 09:22:39 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_vcf.sh	Thu Dec 10 09:22:39 2015 -0500
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+OUTPUT=$1
+shift
+VCF=$1
+shift
+FILTERS=$@
+
+FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
+
+CMD="filter_vcf.py --vcf $VCF --filters $FILTERS --output $OUTPUT"
+
+echo "CMD: "$CMD
+eval $CMD