To simulate genotypes for case individuals drawn from subpopulation c = 1, ...,C, allele counts 0, 1, and 2 are assigned with probabilities (1−pc)2t,2ψpc(1−pc)tandψ2pc2t respectively, where pc is the minor allele frequency in population c for controls, t=(1−pc)2+2ψpc(1−pc)+ψ2pc2 and ψ is the GRR. For the trio data, there are 10 family types. For every locus or marker, l, and c, a family type was generated using the probabilities found in Table I. These probabilities are based on the assumption of the Hardy–Weinberg equilibrium in the parental generation.
