# HG changeset patch
# User devteam
# Date 1393220077 18000
# Node ID c803b1068fa6699e91b9d7fafac8080935067c56
# Parent  f8f98876c3ce292099a8e4618026e0f5710999cc
Uploaded

diff -r f8f98876c3ce -r c803b1068fa6 mergevcf_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergevcf_wrapper.sh	Mon Feb 24 00:34:37 2014 -0500
@@ -0,0 +1,17 @@
+#!/bin/bash
+#index all vcfs
+args=""
+for file in  ${*:2}
+do
+	cp $file $file.vcf
+	java -Xmx1500m  -jar `dirname $0`/igvtools.jar index $file.vcf
+	args="$args I=$file.vcf"
+done
+
+eval java -Xmx2G -jar $JAVA_JAR_PATH/MergeVcfs.jar QUIET=True O=$1 $args
+
+for file in  ${*:2}
+do
+	rm -f $file.vcf
+	rm -f $file.vcf.idx
+done