and MULTIMIX [Churchhouse and Marchini, 2013] methods. Phased reference panel data was used with the MULTIMIX software, and local ancestry estimates when using phased and unphased genotype data for the GAW18 sample individuals were compared. For the local ancestry analysis with the LAMP software, Chen et al [2013] identified a set of 522 ancestry informative markers (AIMs) that were in low linkage disequilibrium (LD) by using genotype and allele frequency data from Hapmap CEU and YRI for European and African ancestries, respectively, as well as allele frequencies for the Mayan (MAY) and Pima (PMA) samples from the Allele FREquency Database (ALFRED) (http://alfred.med.yale.edu/alfred/AboutALFRED.asp) for Native American ancestry.
