Mercurial > repos > devteam > picard1106
annotate mergevcf_wrapper.sh @ 153:5d881472c379 draft default tip
mm
| author | Rayan Chikhi <chikhi@psu.edu> |
|---|---|
| date | Mon, 21 Jul 2014 16:36:03 -0400 |
| parents | c803b1068fa6 |
| children |
| rev | line source |
|---|---|
| 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 |