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Allele-specific likelihood-based test for the inbreeding among samples

Category Annotation Modules

VCF Field INFO (variant-level)

Type AS_StandardAnnotation

Header definition line
  • INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient">

  • Overview

    This annotation estimates whether there is evidence of inbreeding in a population. The higher the score, the higher the chance that there is inbreeding.

    Statistical notes

    The calculation is a continuous generalization of the Hardy-Weinberg test for disequilibrium that works well with limited coverage per sample. The output is the F statistic from running the HW test for disequilibrium with PL values. See the method document on statistical tests for a more detailed explanation of this statistical test.


    • The inbreeding coefficient can only be calculated for cohorts containing at least 10 founder samples.
    • This annotation can take a valid pedigree file to specify founders. If not specified, all samples will be considered as founders.

    Related annotations

    • InbreedingCoeff outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • ExcessHet estimates excess heterozygosity in a population of samples.

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