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Merge pull request #651 from broadinstitute/cww_fastSiblingIBD 

Created a new tool, SiblingIBD, which finds Identical-By-Descent regions...
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Eric Banks 2014-06-13 09:51:33 -04:00
parent fbc75c8e14 ba1d23e535
commit 164d270447
1 changed files with 9 additions and 1 deletions
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10
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java
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@ -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());