a desired disease prevalence , individuals with liabilities greater than the quantile were classified as cases and others were classified as controls. Then equal numbers of cases and controls were drawn from the cohort as a GWAS data set. When simulating two diseases simultaneously, we simulated two disjoint cohorts with the same set of SNPs. To reflect the pleiotropy effects between the two diseases, risk SNPs () were chosen to be shared by the two diseases. The annotation status of each risk and non-risk SNP was simulated from a Bernoulli distribution with probability of and , respectively.
