We made several simplifying assumptions in the above simulations that do not hold in real data sets. These include a single SNP per ancestry block, no genotyping error, no local ancestry inference error, no LD, a normal or uniform distribution of ancestry proportion, continuous phenotypes, and that the effect size distribution of common and rare variants used in computing FSTC was identical. To address these complexities, we took the approach of using real genotypes and simulating phenotypes. We simulated continuous and case-control phenotypes over 5,129 individuals (excluding close relatives) from the CARe cohort (see Online Methods). Although phenotypes were generated from SNPs sampled across all genotyped SNPs, we only used local ancestry information from every 5th SNP.
