diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 12a657d7c..713b4c8cc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -234,8 +234,7 @@ public class PhaseByTransmission extends RodWalker { finalGenotypes.add(father); finalGenotypes.add(child); - if (mother.isCalled() && !father.isCalled() && !child.isCalled()) { - } else { + if (mother.isCalled() && father.isCalled() && child.isCalled()) { ArrayList possibleMotherGenotypes = createAllThreeGenotypes(ref, alt, mother); ArrayList possibleFatherGenotypes = createAllThreeGenotypes(ref, alt, father); ArrayList possibleChildGenotypes = createAllThreeGenotypes(ref, alt, child);