From ba1d23e53591679a0c09a85bf62b1f2a28252ffc Mon Sep 17 00:00:00 2001 From: Chris Whelan Date: Wed, 7 May 2014 10:10:52 -0400 Subject: [PATCH] Created a new tool, SiblingIBD, which finds Identical-By-Descent regions in two siblings. -When parental genotypes are available, implements an HMM on genotype observations in the quartet. -Outputs IBD regions as well as per-site posterior probabilities of being in each IBD state. -Includes an experimental heuristic based mode for when parental genotypes are not available. -Made a method in MendelianViolation public static to reuse code. -Added the mockito library to private/gatk-tools-private/pom.xml --- .../broadinstitute/gatk/utils/MendelianViolation.java | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java index eee1f4752..75666a7e8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java @@ -373,7 +373,15 @@ public class MendelianViolation { } } - private boolean isViolation(Genotype gMom, Genotype gDad, Genotype gChild) { + /** + * Evaluate the genotypes of mom, dad, and child to detect Mendelian violations + * + * @param gMom + * @param gDad + * @param gChild + * @return true if the three genotypes represent a Mendelian violation; false otherwise + */ + public static boolean isViolation(final Genotype gMom, final Genotype gDad, final Genotype gChild) { //1 parent is no "call if(!gMom.isCalled()){ return (gDad.isHomRef() && gChild.isHomVar()) || (gDad.isHomVar() && gChild.isHomRef());