To simulate data from realistic cohort-based association studies, we first generated dense genotype data from a coalescent model. Then, conditional on these genotypes, we simulated quantitative trait data for all individuals in each cohort. In order to mimic the marker density from a GWA study, we masked a fraction of the SNPs and then imputed these genotypes, conditional on a set of simulated reference haplotypes and the remaining observed SNPs. Finally, we performed analyses to test for association between imputed genotype and phenotype.
