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Merge pull request #418 from broadinstitute/eb_fix_liftover_script 

Fixing the liftover script to not require strict VCF header validation.
This commit is contained in:
Eric Banks 2013-11-07 06:04:56 -08:00
parent f67c3a1b4e 2fc40a0aed
commit f15355856a
2 changed files with 4 additions and 3 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@ -118,7 +119,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), VariantContextWriterFactory.NO_OPTIONS);
writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER));
writer.writeHeader(vcfHeader);
}

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 -V:variant $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 $newRef.dict -U LENIENT_VCF_PROCESSING";
if ($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 -V:variant $sorted_vcf -o $out";
$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -V:variant $sorted_vcf -o $out -U LENIENT_VCF_PROCESSING";
system($cmd) == 0 or quit("The filtering step failed. Please correct the necessary errors before retrying.");
# clean up