Local ancestry accuracy in simulations of African Americans, Mexicans and Puerto Ricans.

Accuracy is reported as mean r2 (haploid accuracy, diploid accuracy). “Array data” denotes that a method was run only on the variants present on the Illumina 1 M genotyping array. “Full genome” denotes methods were run using all the variants. RFMix requires phased haplotype input that was phased using Beagle; all other methods received unphased genotype data as input. Correlation values are the mean squared correlation across SNPs of the true vs. inferred ancestry across individuals. Accuracy is reported as mean r2 (haploid accuracy, diploid accuracy). LAMP-LD and MULTIMIX were optimized to run with genotyping array data, possibly explaining the steep drop in accuracy when they are run using full sequencing data.