Mercurial > repos > devteam > picard1106

view mergevcf_wrapper.sh @ 92:29447daa90e0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author devteam
date Mon, 24 Feb 2014 00:42:27 -0500
parents c803b1068fa6
children
line wrap: on
line source

#!/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