Showing tool doc from version 4.0.4.0 | The latest version is 4.1.4.1
4.0.4.0

AS_InbreedingCoeff

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 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.

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.

Return to top

See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum

GATK version 4.0.4.0 built at 23-40-2018 11:40:56.