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Likelihood-based test for the inbreeding among samples

Category Variant Annotations

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation

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  • INFO=

  • 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 a Phred-scaled p-value derived 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.


    Note that the Inbreeding Coefficient can only be calculated for cohorts containing at least 10 founder samples.

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    GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA