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Bug fix, wherein triple-hets after genotype refinement need to be left unphased, not just prior to refinement

This commit is contained in:
Kiran V Garimella 2011-07-26 17:43:43 -04:00
parent 36daaa7bda
commit 412c466de6
1 changed files with 8 additions and 6 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -234,7 +234,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
finalGenotypes.add(father); finalGenotypes.add(father);
finalGenotypes.add(child); finalGenotypes.add(child);
if (mother.isCalled() && father.isCalled() && child.isCalled() && !(mother.isHet() && father.isHet() && child.isHet())) { if (mother.isCalled() && father.isCalled() && child.isCalled()) {
ArrayList<Genotype> possibleMotherGenotypes = createAllThreeGenotypes(ref, alt, mother); ArrayList<Genotype> possibleMotherGenotypes = createAllThreeGenotypes(ref, alt, mother);
ArrayList<Genotype> possibleFatherGenotypes = createAllThreeGenotypes(ref, alt, father); ArrayList<Genotype> possibleFatherGenotypes = createAllThreeGenotypes(ref, alt, father);
ArrayList<Genotype> possibleChildGenotypes = createAllThreeGenotypes(ref, alt, child); ArrayList<Genotype> possibleChildGenotypes = createAllThreeGenotypes(ref, alt, child);
@ -265,6 +265,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
} }
} }
if (!(bestMotherGenotype.isHet() && bestFatherGenotype.isHet() && bestChildGenotype.isHet())) {
Map<String, Object> attributes = new HashMap<String, Object>(); Map<String, Object> attributes = new HashMap<String, Object>();
attributes.putAll(bestChildGenotype.getAttributes()); attributes.putAll(bestChildGenotype.getAttributes());
attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm); attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm);
@ -272,6 +273,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
finalGenotypes = getPhasedGenotypes(bestMotherGenotype, bestFatherGenotype, bestChildGenotype); finalGenotypes = getPhasedGenotypes(bestMotherGenotype, bestFatherGenotype, bestChildGenotype);
} }
}
return finalGenotypes; return finalGenotypes;
} }