# HardyWeinberg

Hardy-Weinberg test for transmission disequilibrium

## Overview

This annotation estimates whether the frequencies of alleles and genotypes in a population stay the same from generation to generation.

### Statistical notes

The output is a Phred-scaled P value. See the method document on statistical tests for a more detailed explanation of the Hardy-Weinberg test.

### Caveats

• This annotation requires multiple samples and a valid pedigree file.
• 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.
• Low confidence genotypes are ignored, which may adversely affect HW ratios. More analysis is needed to determine the right thing to do when the genotyper cannot decide whether a given sample is heterozygous or homozygous variant.