Mercurial > repos > ulfschaefer > phephenix

diff filter_vcf.sh @ 0:45ff0fc972e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ulfschaefer
date Thu, 21 Apr 2016 05:52:44 -0400
parents
children a6079f6217f5
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_vcf.sh	Thu Apr 21 05:52:44 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