Phred-scaled p-value for exact test of excess heterozygosity
INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
This annotation estimates excess heterozygosity in a population of samples. It is related to but distinct from InbreedingCoeff, which estimates evidence for inbreeding in a population. ExcessHet scales more reliably to large cohort sizes.
This annotation is a one-sided phred-scaled p-value using an exact test of the Hardy-Weinberg Equilibrium. The null hypothesis is that the number of heterozygotes follows the Hardy-Weinberg Equilibrium. The p-value is the probability of getting the same or more heterozygotes as was observed, given the null hypothesis.
The implementation used is adapted 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.
The p-value is calculated exactly by using the Levene-Haldane distribution. This implementation also uses a mid-p correction as described by Graffelman, J. & Moreno, V. (2013). The mid p-value in exact tests for Hardy-Weinberg equilibrium. Statistical Applications in Genetics and Molecular Biology, 12(4), pp. 433-448.
GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.