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Added recordOriginalLocation option perl script 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4931 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-01-04 19:52:50 +00:00
parent 96729acd0d
commit 8de33924e8
1 changed files with 6 additions and 4 deletions
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10
perl/liftOverVCF.pl
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@ -12,16 +12,18 @@ my $newRef = undef;
my $oldRef = undef;
my $out = undef;
my $tmp = "/tmp";
my $recordOriginalLocation = undef;
GetOptions( "vcf=s" => \$in,
"gatk=s" => \$gatk,
"chain=s" => \$chain,
"newRef=s" => \$newRef,
"oldRef=s" => \$oldRef,
"out=s" => \$out,
"tmp=s" => \$tmp);
"tmp=s" => \$tmp,
"recordOriginalLocation" => \$recordOriginalLocation);
if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out ) {
print "Usage: liftOverVCF.pl\n\t-vcf \t\t<input vcf>\n\t-gatk \t\t<path to gatk trunk>\n\t-chain \t\t<chain file>\n\t-newRef \t<path to new reference prefix; we will need newRef.dict, .fasta, and .fasta.fai>\n\t-oldRef \t<path to old reference prefix; we will need oldRef.fasta>\n\t-out \t\t<output vcf>\n\t-tmp \t\t<temp file location; defaults to /tmp>\n";
if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out || !defined($recordOriginalLocation)) {
print "Usage: liftOverVCF.pl\n\t-vcf \t\t<input vcf>\n\t-gatk \t\t<path to gatk trunk>\n\t-chain \t\t<chain file>\n\t-newRef \t<path to new reference prefix; we will need newRef.dict, .fasta, and .fasta.fai>\n\t-oldRef \t<path to old reference prefix; we will need oldRef.fasta>\n\t-out \t\t<output vcf>\n\t-tmp \t\t<temp file location; defaults to /tmp>\n\t-recordOriginalLocation \t\t<Should we record what the original location was in the INFO field?; defaults to false>\n";
print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /humgen/1kg/reference/human_b36_both\n";
exit(1);
}
@ -34,7 +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 -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict -recordOriginalLocation $recordOriginalLocation";
system($cmd);
# we need to sort the lifted over file now