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Corner case fix for indel GL computation: sometimes (depending on surrounding context) reads which are not informative of two candidate haplotypes end up having marginally higher likelihoods with one haplotype as opposed to another, depending on uncertainty on alignments in surrounding regions. So, a sample whose GL is -0.0001,-0.0005,-0.001 may have its genotype set to 1/1 due to this statistical noise. We already have a tolerance comparing max(gl)-min(gl) to avoid genotyping, so this tolerance is now increased from 0.001 to 0.1 (equivalent to 1 PL unit) to avoid genotyping a sample if all PLs are within this threshold. Changed 2 integration test md5s that hit this case.

This commit is contained in:
Guillermo del Angel 2012-04-26 10:15:26 -04:00
parent ab2a952ad1
commit 972d6531b6
2 changed files with 3 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -1153,7 +1153,7 @@ public class VariantContextUtils {
}
private static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
public static final double SUM_GL_THRESH_NOCALL = -0.001; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
/**
* subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately)

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

@ -327,13 +327,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("0b388936022539530f565da14d5496d3"));
Arrays.asList("9c9ff13dba0898e905ac9e23d30a24b6"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("537dd9b4174dc356fb13d8d3098ad602"));
Arrays.asList("300e6274f8c1ce6a577eb06e5b56de90"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}