The method is described in kim2011 and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates.
The likelihood of the sequencing data of individuals for sites can be described through the allele frequencies and the type specific error rates
by summing over the unknown genotypes . The genotype likelihood relies on the type specific error rates (see kim2011 p.14 for details). The type specific error rates are obtain along site the allele frequencies by