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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
This commit is contained in:
andrewk 2010-01-07 15:30:04 +00:00
parent 076481f786
commit 431e9c2c8b
1 changed files with 8 additions and 3 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/HapMap2VCF.java
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.HapMapGenotypeROD; import org.broadinstitute.sting.gatk.refdata.HapMapGenotypeROD;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; 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.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.genotype.vcf.*; import org.broadinstitute.sting.utils.genotype.vcf.*;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
@ -42,6 +43,7 @@ public class HapMap2VCF extends RodWalker<Integer, Integer> {
for ( ReferenceOrderedDatum rod : tracker.getAllRods() ) { for ( ReferenceOrderedDatum rod : tracker.getAllRods() ) {
if ( rod instanceof HapMapGenotypeROD ) { if ( rod instanceof HapMapGenotypeROD ) {
GenomeLoc loc = context.getLocation();
HapMapGenotypeROD hapmap_rod = (HapMapGenotypeROD) rod; 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 // 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<Integer, Integer> {
vcfWriter.writeHeader(sample_id_set, hInfo); vcfWriter.writeHeader(sample_id_set, hInfo);
} }
// Get reference base and locus // Get reference base
Character ref_allele = ref.getBase(); Character ref_allele = ref.getBase();
GenomeLoc loc = hapmap_rod.getLocation();
VCFVariationCall variation = new VCFVariationCall(ref_allele, loc, Variation.VARIANT_TYPE.SNP); VCFVariationCall variation = new VCFVariationCall(ref_allele, loc, Variation.VARIANT_TYPE.SNP);
// Print each sample's genotype info // Print each sample's genotype info
@ -85,7 +86,11 @@ public class HapMap2VCF extends RodWalker<Integer, Integer> {
// add each genotype to VCF record and write it // add each genotype to VCF record and write it
variation.setGenotypeCalls(genotype_calls); 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);
} }
} }