Documentation

HardyWeinberg

Hardy-Weinberg test for disequilibrium

Category Variant Annotations

VCF Field INFO (variant-level)

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.


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GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA