# HG changeset patch
# User ulfschaefer
# Date 1466073577 14400
# Node ID e2ee6acf8752632ff53c5b78ad699ccd846ea318
# Parent  7ccbcc8608fa29082277f2becaf2284c9116797f
Uploaded

diff -r 7ccbcc8608fa -r e2ee6acf8752 filter_vcf.sh
--- a/filter_vcf.sh	Thu Jun 16 06:39:26 2016 -0400
+++ b/filter_vcf.sh	Thu Jun 16 06:39:37 2016 -0400
@@ -6,13 +6,15 @@
 shift
 VCF=$1
 shift
+REF=$1
+shift
 ONLYGOOD=$1
 shift
 FILTERS=$@
 
 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
 
-CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT"
+CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT --reference $REF"
 
 if [ $ONLYGOOD != "NOTTHERE" ]; then
     CMD="$CMD --only-good"