Due to differences in genotyping arrays, RFMix (V1.5.4) (Maples, Gravel, Kenny, & Bustamante, 2013) was used to estimate local African ancestry in each cohort separately. RFMix is a discriminative modeling approach that uses random forests trained on reference samples. Ninety-nine CEU and 99 YRI samples from 1000 Genomes Phase 3 were used as European and African reference samples, respectively, as recommended by RFMix. Only genotyped, high quality variants (defined as missing rate <0.05, Hardy-Weinberg P-values >0.001, and MAF >3%) were included to improve inference accuracy. SHAPEIT2 (Delaneau et al., 2013) was used for haplotype phasing, then RFMix was used to estimate the number of African alleles at each locus (i.e., 0, 1 or 2 copies of African alleles, referred as local African ancestry). For each individual, global African ancestry was also calculated as the average percentage of African ancestry across the entire genome.
