genotypes from individual i at SNP s(gis) were then generated by drawing from the binomial distributions with allele frequencies specified by the local ancestry for that individual at that SNP. That is, if the individual had two copies of ancestry from P0 at SNP s then two draws from a binomial with parameter p0s were used. To create a phenotype we first selected Nr causal variants where r is the proportion of causal variants. Effect sizes were drawn from the normal distribution N(0,h2/(Nr)) and the genetic element of the phenotype was generated by taking the inner product of the causal variants, normalized to have mean 0 and variance 1, and the effect sizes for the variants. Normally distributed random noise was added such that the total heritability in the population was h2.
