Phred-scaled p-value for exact test of excess heterozygosity

Category Annotation Modules

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation

Header definition line
  • INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">

  • Overview

    This annotation estimates excess heterozygosity in a population of samples. It is related to but distinct from InbreedingCoeff, which estimates evidence for inbreeding in a population. ExcessHet scales more reliably to large cohort sizes.

    Statistical notes

    This annotation is a one-sided phred-scaled p-value using an exact test of the Hardy-Weinberg Equilibrium. The null hypothesis is that the number of heterozygotes follows the Hardy-Weinberg Equilibrium. The p-value is the probability of getting the same or more heterozygotes as was observed, given the null hypothesis.

    The implementation used is adapted from Wigginton JE, Cutler DJ, Abecasis GR. A Note on Exact Tests of Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 2005;76(5):887-893.

    The p-value is calculated exactly by using the Levene-Haldane distribution. This implementation also uses a mid-p correction as described by Graffelman, J. & Moreno, V. (2013). The mid p-value in exact tests for Hardy-Weinberg equilibrium. Statistical Applications in Genetics and Molecular Biology, 12(4), pp. 433-448.


    • The annotation is not accurate for very small p-values. Beyond 1.0E-16 there is no guarantee that the p-value is accurate, just that it is in fact smaller than 1.0E-16.
    • For multiallelic sites, all non-reference alleles are treated as a single alternate allele.

    Related annotations

    • InbreedingCoeff estimates whether there is evidence of inbreeding in a population
    • AS_InbreedingCoeff outputs an allele-specific version of the InbreedingCoeff annotation.

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    GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.