zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fixed a small feature/bug that I introduced with the spanning deletions genotyping. 

In the case where there's a low quality SNP under a spanning deletion in the gvcfs:
if the SNP is not genotyped by GenotypeGVCFs (because it's just noise) we were still
emitting a record with just the symbolic DEL allele (because that allele is high quality).

We no longer do that.
This commit is contained in:
Eric Banks 2015-05-13 11:10:23 -04:00
parent 7a75f4ae79
commit c752b9bca6
2 changed files with 22 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
View File

@ -261,7 +261,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
// only re-genotype polymorphic sites
if ( result.isVariant() ) {
VariantContext regenotypedVC = genotypingEngine.calculateGenotypes(result);
if ( regenotypedVC == null) {
if ( ! isProperlyPolymorphic(regenotypedVC) ) {
if (!INCLUDE_NON_VARIANTS)
return null;
}
@ -295,6 +295,16 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
return result;
}
/**
* Determines whether the provided VariantContext has real alternate alleles
*
* @param vc the VariantContext to evaluate
* @return true if it has proper alternate alleles, false otherwise
*/
private boolean isProperlyPolymorphic(final VariantContext vc) {
return ( vc != null && !vc.isSymbolic() );
}
/**
* Add genotyping-based annotations to the new VC
*

11
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
View File

@ -480,4 +480,15 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
spec.disableShadowBCF();
executeTest("testMultipleSpanningDeletionsMD5", spec);
}
@Test(enabled = true)
public void testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.delOnly.g.vcf",
1,
Arrays.asList("46169d08f93e5ff57856c7b64717314b"));
spec.disableShadowBCF();
executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
}
}