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Fixed recordOriginalLocation option to work properly 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4932 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-01-04 19:58:13 +00:00
parent 8de33924e8
commit d9270b2363
1 changed files with 4 additions and 1 deletions
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5
perl/liftOverVCF.pl
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@ -36,7 +36,10 @@ my $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
# lift over the file # lift over the file
print "Lifting over the vcf..."; print "Lifting over the vcf...";
my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict -recordOriginalLocation $recordOriginalLocation"; my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
if ($recordOriginalLocation) {
$cmd .= " -recordOriginalLocation";
}
system($cmd); system($cmd);
# we need to sort the lifted over file now # we need to sort the lifted over file now