PostFreq

Estimator from genotype probabilities

If the genotype probabilities are known the frequencies can be estimated by summing up the posterior probabilities $p(G=g|D)$ where $D$ is the sequencing data and $g\in{0,1,2}$ the allele count of the minor allele. The frequency estimate

$$ \hat{f}=\frac{1}{2N}\sum_i^N \left(2p(G=2|D)+p(G=1|D)\right) $$