Data preparation and analysis for 1000Genomes samples: The full 1000Genomes dataset was first filtered to include only bi-allelic single nucleotide polymorphisms (SNPs) with greater than 0.1% minor allele frequency. In order to calculate principal components across 1000Genomes genotypes, we used second generation PLINK49 to obtain variants in approximate linkage equilibrium, and we also removed the MHC region of chromosome 6 (25–35 Mb) and the large inversion region on chromosome 8 (7–13 Mb). We then calculated 20 PCs across all individuals.
