Genotype Likelihood based Inbreeding Coefficient
Inbreeding Coefficient is an important statistic in the study of genetic variants. This page details a method to estimate inbreeding coefficients from genotype likelihoods in NGS data.
The inbreeding coefficient is a measure of deviation from the Hardy Weinberg Equilibrium in terms of the excess of heterozygotes observed. A value of 0 implies no deviation, a negative value implies an excess of heterozygotes and a positive value implies an excess of homozygotes. ranges from -1 to 1.
The following equation gives the estimate of F where the observed genotypes are available. is the genotype composed of alleles and for the th individual. is the estimated genotype allele frequency for genotype under HWE assumption. is an indicator function for heterozygote genotypes.
The following equation gives the estimate of F where genotype likelihoods are available. is the genotype likelihood for individual given genotype . This is basically the probability of observing the reads in individual assuming is the underlying true genotype for that particular locus.
Adrian with much help from Hyun.
This is implemented in vt.
This page is maintained by Adrian.