Likelihood-based test for the consanguinity among samples (InbreedingCoeff)
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.
ExcessHet also describes the heterozygosity of the called samples, giving a probability of excess heterozygosity being observed
GATK version 220.127.116.11 built at 10-58-2018 11:58:10.