Allele-specific likelihood-based test for the consanguinity among samples (AS_InbreedingCoeff)
Category Variant Annotations
OverviewAllele-specific likelihood-based test for the inbreeding among samples
This annotation estimates whether there is evidence of inbreeding in a population. The higher the score, the higher the chance that there is inbreeding.
The calculation is a continuous generalization of the Hardy-Weinberg test for disequilibrium that works well with limited coverage per sample. The output is the F statistic 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 can only be calculated for cohorts containing at least 10 founder samples.
- This annotation can take a valid pedigree file to specify founders. If not specified, all samples will be considered as founders.
- InbreedingCoeff outputs a version of this annotation that includes all alternate alleles in a single calculation.
- ExcessHet estimates excess heterozygosity in a population of samples.
GATK version 220.127.116.11-SNAPSHOT built at Mon, 19 Oct 2020 11:41:12 -0400.