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The SNP genotype concordance module is now more comprehensive. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2330 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-11 18:34:33 +00:00
parent 590aeee7d2
commit 2ea7632b76
2 changed files with 36 additions and 27 deletions
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59
java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java
View File

@ -34,12 +34,19 @@ public class SNPGenotypeConcordance implements ConcordanceType {
Genotype call1 = samplesToRecords.get(sample1);
Genotype call2 = samplesToRecords.get(sample2);
// the only reason they would be null is a lack of coverage
if ( call1 == null || call2 == null ) {
if ( call1 != null && call1.isPointGenotype() && (10.0 * call1.getNegLog10PError()) >= Qscore )
return "set1ConfidentVariantSet2NoCoverage";
else if ( call2 != null && call2.isPointGenotype() && (10.0 * call2.getNegLog10PError()) >= Qscore )
return "set1NoCoverageSet2ConfidentVariant";
if ( call1 != null && call1.isPointGenotype() ) {
if ( 10.0 * call1.getNegLog10PError() >= Qscore )
return "set1ConfidentSet2NoCall";
else
return "set2NoCall";
}
else if ( call2 != null && call2.isPointGenotype() ) {
if (10.0 * call2.getNegLog10PError() >= Qscore )
return "set1NoCallSet2Confident";
else
return "set1NoCall";
}
return null;
}
@ -51,30 +58,32 @@ public class SNPGenotypeConcordance implements ConcordanceType {
// are they both variant SNPs?
if ( call1.isPointGenotype() && call2.isPointGenotype() ) {
// are they both confident calls?
if ( confidence1 >= Qscore && confidence2 >= Qscore ) {
// same genotype
if ( genotype1.equals(genotype2) )
return "sameConfidentVariant";
// are they confident calls?
boolean conf1 = confidence1 >= Qscore;
boolean conf2 = confidence2 >= Qscore;
boolean confCombo = !conf1 && !conf2 && confidence1 + confidence2 >= Qscore;
// same allele, different genotype
else if ( sameVariantAllele(genotype1, genotype2, ref.getBase()) )
return "sameVariantAlleleDifferentGenotype";
StringBuffer result = new StringBuffer("");
if ( conf1 && conf2 )
result.append("bothConfident");
else if ( confCombo )
result.append("confidentWhenCombined");
else if ( conf1 ||conf2 )
result.append("onlyOneConfident");
else
result.append("neitherConfident");
// different variant allele
else
return "differentVariantAllele";
}
result.append("_");
// confident only when combined
else if ( confidence1 < Qscore && confidence2 < Qscore && confidence1 + confidence2 >= Qscore ) {
return "confidentVariantWhenCombined";
}
// are they the same genotype
if ( genotype1.equals(genotype2) )
result.append("sameGenotype");
else if ( sameVariantAllele(genotype1, genotype2, ref.getBase()) )
result.append("differentGenotypeSameVariantAllele");
else
result.append("differentVariantAllele");
// only one is confident variant
else if ( (confidence1 < Qscore && confidence2 >= Qscore) || (confidence1 >= Qscore && confidence2 < Qscore) ) {
return "bothVariantOnlyOneIsConfident";
}
return result.toString();
}
// one is variant and the other is ref

4
java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
View File

@ -22,7 +22,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
public void testSNPConcordance() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1,
Arrays.asList("c21d59fc3194c39c662d2e74b53dcf9c"));
Arrays.asList("8a17c93572a2c498feeaf8ba172d40d6"));
executeTest("testSNPConcordance", spec);
}
@ -38,7 +38,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
public void testMulti() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SimpleVenn -CT NWayVenn -CT SNPGenotypeConcordance:qscore=5", 1,
Arrays.asList("9bcc83aadac00a160cef20e7126368ee"));
Arrays.asList("4e0f768389028dbd09266ee1802ccd3b"));
executeTest("testMulti", spec);
}
}