Showing docs for version 3.7-0
InbreedingCoeff
Likelihood-based test for the inbreeding among samples
Category
Annotation Modules
VCF Field
INFO (variant-level)
Type
StandardAnnotation, ActiveRegionBasedAnnotation, ReducibleAnnotation
Header definition line
INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
Overview
This 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 is used in variant filtering, but may not be appropriate for that purpose if the cohort being analyzed contains many closely related individuals.
- This annotation can take a valid pedigree file to specify founders.
Related annotations
- AS_InbreedingCoeff outputs an allele-specific version of this annotation.
- ExcessHet estimates excess heterozygosity in a population of samples.