Mercurial > repos > ulfschaefer > phephenix

diff filter_vcf.sh @ 0:cb29f95c7b88 draft

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author ulfschaefer
date Mon, 09 May 2016 09:27:06 -0400
parents
children e2ee6acf8752
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_vcf.sh	Mon May 09 09:27:06 2016 -0400
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# echo $@
+
+OUTPUT=$1
+shift
+VCF=$1
+shift
+ONLYGOOD=$1
+shift
+FILTERS=$@
+
+FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
+
+CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT"
+
+if [ $ONLYGOOD != "NOTTHERE" ]; then
+    CMD="$CMD --only-good"
+fi
+
+echo "CMD: "$CMD
+eval $CMD