Likelihood-based test for the consanguinity among samples (InbreedingCoeff)
Category Variant Annotations
OverviewLikelihood-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.
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.
- 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.
ExcessHet also describes the heterozygosity of the called samples, giving a probability of excess heterozygosity being observed
GATK version 18.104.22.168 built at Sat, 23 Nov 2019 17:12:18 -0500.