From 431e9c2c8b55da85417e8b67e5c7a867da49678f Mon Sep 17 00:00:00 2001 From: andrewk Date: Thu, 7 Jan 2010 15:30:04 +0000 Subject: [PATCH] Add dbSNP ID to VCF output records git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2536 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/variantstovcf/HapMap2VCF.java | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/HapMap2VCF.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/HapMap2VCF.java index 79863e020..3e9250fca 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/HapMap2VCF.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/HapMap2VCF.java @@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.HapMapGenotypeROD; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; +import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.genotype.vcf.*; import org.broadinstitute.sting.utils.genotype.Variation; @@ -42,6 +43,7 @@ public class HapMap2VCF extends RodWalker { for ( ReferenceOrderedDatum rod : tracker.getAllRods() ) { if ( rod instanceof HapMapGenotypeROD ) { + GenomeLoc loc = context.getLocation(); HapMapGenotypeROD hapmap_rod = (HapMapGenotypeROD) rod; // If this is the first time map is called, we need to fill out the sample_ids from the rod @@ -62,9 +64,8 @@ public class HapMap2VCF extends RodWalker { vcfWriter.writeHeader(sample_id_set, hInfo); } - // Get reference base and locus + // Get reference base Character ref_allele = ref.getBase(); - GenomeLoc loc = hapmap_rod.getLocation(); VCFVariationCall variation = new VCFVariationCall(ref_allele, loc, Variation.VARIANT_TYPE.SNP); // Print each sample's genotype info @@ -85,7 +86,11 @@ public class HapMap2VCF extends RodWalker { // add each genotype to VCF record and write it variation.setGenotypeCalls(genotype_calls); - vcfWriter.addMultiSampleCall(genotype_calls, new VCFVariationCall(ref_allele, loc, Variation.VARIANT_TYPE.SNP)); + VCFVariationCall call = new VCFVariationCall(ref_allele, loc, Variation.VARIANT_TYPE.SNP); + rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getTrackData("dbsnp", null)); + if (dbsnp != null) + call.setID(dbsnp.getRS_ID()); + vcfWriter.addMultiSampleCall(genotype_calls, call); } }