This method of estimating the two allele frequencies is conceptually much simpler than the one described in [31], which uses a Markov chain Monte Carlo approach to estimate the frequencies both from cases and controls. Differences between these frequencies is not an important concern given the overwhelmingly large number of controls genotyped and given that we already know the average frequency of European ancestry in African Americans. Following the notation in [32], we set the emission probabilities ejk(t) for j,k=0..2, where j indicates the number of chromosomes of European ancestry at a given locus and k indicates the number of non reference alleles observed at that locus, as
