Likelihood-based test for the consanguinity among samples (InbreedingCoeff)

Category Variant Annotations

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Overview

Likelihood-based test for the consanguinuity among samples

This annotation estimates whether there is evidence of consanguinuity in a population. The higher the score, the higher the chance that some samples are related. If samples are known to be related, a pedigree file can be provided so that the calculation is only performed on founders and offspring are excluded.

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.

Caveats

• The Inbreeding Coefficient annotation can only be calculated for cohorts containing at least 10 founder samples.
• The Inbreeding Coefficient annotation can only be calculated for diploid samples.

Related annotations

ExcessHet also describes the heterozygosity of the called samples, giving a probability of excess heterozygosity being observed

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GATK version 4.0.10.0 built at 25-30-2019 05:30:15.