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InbreedingCoeff

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

Category Variant Annotations


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 4.0.4.0 built at 23-40-2018 11:40:56.