Showing tool doc from version 4.0.4.0 | The latest version is 4.1.2.0

ExcessHet

Phred-scaled p-value for exact test of excess heterozygosity (ExcessHet)

Category Variant Annotations


Overview

Phred-scaled p-value for exact test of excess heterozygosity.

This annotation estimates the probability of the called samples exhibiting excess heterozygosity with respect to the null hypothesis that the samples are unrelated. The higher the score, the higher the chance that the variant is a technical artifact or that there is consanguinuity among the samples. In contrast to Inbreeding Coefficient, there is no minimal number of samples for this annotation. 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.

Statistical notes

This annotation uses the implementation from Wigginton JE, Cutler DJ, Abecasis GR. A Note on Exact Tests of Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 2005;76(5):887-893.

Caveat

The Excess Heterozygosity annotation can only be calculated for diploid samples.

Related annotations

InbreedingCoeff also describes the heterozygosity of the called samples, though without explicitly taking into account the number 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.