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update to use new rod syntax 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4119 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-25 20:21:53 +00:00
parent 4678613893
commit a7af605d95
1 changed files with 2 additions and 2 deletions
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4
perl/liftOverVCF.pl
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@ -34,7 +34,7 @@ my $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
# lift over the file
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";
my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
system($cmd);
# we need to sort the lifted over file now
@ -61,7 +61,7 @@ close(SORTED);
# Filter the VCF for bad records
print "\nFixing/removing bad records...\n";
$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B variant,vcf,$sorted_vcf -o $out";
$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $sorted_vcf -o $out";
system($cmd);
# clean up