Mercurial > repos > devteam > picard1106
annotate mergevcf_wrapper.sh @ 150:896709401435 draft
dummy commit to attempt to merge multiple heads
author | Rayan Chikhi <chikhi@psu.edu> |
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date | Mon, 21 Jul 2014 16:28:40 -0400 |
parents | c803b1068fa6 |
children |
rev | line source |
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88 | 1 #!/bin/bash |
2 #index all vcfs | |
3 args="" | |
4 for file in ${*:2} | |
5 do | |
6 cp $file $file.vcf | |
7 java -Xmx1500m -jar `dirname $0`/igvtools.jar index $file.vcf | |
8 args="$args I=$file.vcf" | |
9 done | |
10 | |
11 eval java -Xmx2G -jar $JAVA_JAR_PATH/MergeVcfs.jar QUIET=True O=$1 $args | |
12 | |
13 for file in ${*:2} | |
14 do | |
15 rm -f $file.vcf | |
16 rm -f $file.vcf.idx | |
17 done |