Allele-specific likelihood-based test for the consanguinity among samples (AS_InbreedingCoeff)
Category Variant Annotations
Overview
Allele-specific likelihood-based test for the inbreeding among samplesThis annotation estimates whether there is evidence of inbreeding in a population. The higher the score, the higher the chance that there is inbreeding.
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 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.
Caveats
- 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.
Related annotations
- 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 4.0.11.0 built at 25-15-2019 03:15:29.
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