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Hardy-Weinberg test for transmission disequilibrium

Category Annotation Modules

VCF Field INFO (variant-level)

Type ExperimentalAnnotation

Header definition line
  • INFO=<ID=HW,Number=1,Type=Float,Description="Phred-scaled p-value for Hardy-Weinberg violation">

  • 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.


    • This annotation requires multiple samples.
    • 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.

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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.