Local ancestry inference (LAI) parameters: LAI was run on each cohort separately using RFMix version 287 (https://github.com/slowkoni/rfmix) with 1 EM iteration and a window size of 0.2 cM. We used the HapMap b37 recombination map86 to inform switches. The -n 5 flag (terminal node size for random forest trees) was included to account for an unequal number of reference individuals per reference population. We additionally used the --reanalyze-reference flag, which recalculates admixture in the reference samples for improved ability to distinguish ancestries.
