HardyWeinberg

Hardy-Weinberg test for disequilibrium

Category Variant Annotations

Annotation type ExperimentalAnnotation

Overview

This annotation calculates the Phred-scaled P value of genotype-based (using GT field) test for Hardy-Weinberg test for disequilibrium.

Caveats

This is an experimental annotation. As such, it is unsupported; we do not make any guarantees that it will work properly, and you use it at your own risk.

Right now we just ignore genotypes that are not confident, but this throws off our HW ratios. More analysis is needed to determine the right thing to do when the genotyper cannot decide whether a given sample is het or hom var.

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.