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Update to the bindings for liftOverVCF.pl (to -V from -B)

This commit is contained in:
Christopher Hartl 2011-09-15 15:33:09 -04:00
parent d369d10593
commit ce73dc4071
1 changed files with 2 additions and 2 deletions
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4
public/perl/liftOverVCF.pl
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@ -36,7 +36,7 @@ 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 -V:variant $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
if ($recordOriginalLocation) {
$cmd .= " -recordOriginalLocation";
}
@ -66,7 +66,7 @@ system($cmd) == 0 or quit("The sorting step failed. Please correct the necessar
# 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 -V:variant $sorted_vcf -o $out";
system($cmd) == 0 or quit("The filtering step failed. Please correct the necessary errors before retrying.");
# clean up