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Bug fix in VQSR so that the VCF index will be created for the recalFile.

This commit is contained in:
Ryan Poplin 2012-06-08 11:51:28 -04:00
parent 2bd48a7351
commit 0a37e19998
2 changed files with 3 additions and 4 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -139,7 +139,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
// Outputs // Outputs
///////////////////////////// /////////////////////////////
@Output(fullName="recal_file", shortName="recalFile", doc="The output recal file used by ApplyRecalibration", required=true) @Output(fullName="recal_file", shortName="recalFile", doc="The output recal file used by ApplyRecalibration", required=true)
protected File recalFile = null;
protected VariantContextWriter recalWriter = null; protected VariantContextWriter recalWriter = null;
@Output(fullName="tranches_file", shortName="tranchesFile", doc="The output tranches file used by ApplyRecalibration", required=true) @Output(fullName="tranches_file", shortName="tranchesFile", doc="The output tranches file used by ApplyRecalibration", required=true)
@ -230,9 +229,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" ); throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
} }
final VCFHeader vcfHeader = new VCFHeader(); recalWriter.writeHeader( new VCFHeader() );
recalWriter = VariantContextWriterFactory.create(recalFile, getMasterSequenceDictionary());
recalWriter.writeHeader(vcfHeader);
} }
//--------------------------------------------------------------------------------------------------------------- //---------------------------------------------------------------------------------------------------------------

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -47,6 +47,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -T VariantRecalibrator" + " -T VariantRecalibrator" +
" -input " + params.inVCF + " -input " + params.inVCF +
" -L 20:1,000,000-40,000,000" + " -L 20:1,000,000-40,000,000" +
" --no_cmdline_in_header" +
" -an QD -an HaplotypeScore -an HRun" + " -an QD -an HaplotypeScore -an HRun" +
" -percentBad 0.07" + " -percentBad 0.07" +
" --minNumBadVariants 0" + " --minNumBadVariants 0" +
@ -92,6 +93,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -T VariantRecalibrator" + " -T VariantRecalibrator" +
" -input " + params.inVCF + " -input " + params.inVCF +
" -L 20:1,000,000-40,000,000" + " -L 20:1,000,000-40,000,000" +
" --no_cmdline_in_header" +
" -an QD -an ReadPosRankSum -an HaplotypeScore" + " -an QD -an ReadPosRankSum -an HaplotypeScore" +
" -percentBad 0.08" + " -percentBad 0.08" +
" -mode INDEL -mG 3" + " -mode INDEL -mG 3" +