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Added optional field DP to VCF output for Mark. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1981 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-06 20:03:22 +00:00
parent f73dd09399
commit 6fdfc97db6
2 changed files with 7 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
View File

@ -138,10 +138,14 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
Map<String, VCFGenotypeCall> genotypeMap = genotypeListToSampleNameMap(genotypes); Map<String, VCFGenotypeCall> genotypeMap = genotypeListToSampleNameMap(genotypes);
// keep track of the total read depth
int totalReadDepth = 0;
for (String name : mHeader.getGenotypeSamples()) { for (String name : mHeader.getGenotypeSamples()) {
if (genotypeMap.containsKey(name)) { if (genotypeMap.containsKey(name)) {
Genotype gtype = genotypeMap.get(name); Genotype gtype = genotypeMap.get(name);
VCFGenotypeRecord record = createVCFGenotypeRecord(params, (VCFGenotypeCall)gtype); VCFGenotypeRecord record = createVCFGenotypeRecord(params, (VCFGenotypeCall)gtype);
totalReadDepth += ((VCFGenotypeCall)gtype).getReadCount();
params.addGenotypeRecord(record); params.addGenotypeRecord(record);
genotypeMap.remove(name); genotypeMap.remove(name);
} else { } else {
@ -157,6 +161,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
} }
Map<String, String> infoFields = getInfoFields((VCFGenotypeLocusData)locusdata, params); Map<String, String> infoFields = getInfoFields((VCFGenotypeLocusData)locusdata, params);
infoFields.put("DP", String.format("%d", totalReadDepth));
double qual = (locusdata == null) ? 0 : ((VCFGenotypeLocusData)locusdata).getConfidence(); double qual = (locusdata == null) ? 0 : ((VCFGenotypeLocusData)locusdata).getConfidence();
// maintain 0-99 based Q-scores // maintain 0-99 based Q-scores

4
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() { public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 50", 1, "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 50", 1,
Arrays.asList("9985a92060b512b5d27b4074faf8b60b")); Arrays.asList("4f14792e79adef415efaf97e946460e3"));
executeTest("testMultiSamplePilot1", spec); executeTest("testMultiSamplePilot1", spec);
} }
@ -51,7 +51,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2() { public void testMultiSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 50", 1, "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 50", 1,
Arrays.asList("394f009c9bad34eb584fa10d133d79e0")); Arrays.asList("e3a701fd5f1fe4a84746f17ad4b3b3c3"));
executeTest("testMultiSamplePilot2", spec); executeTest("testMultiSamplePilot2", spec);
} }