Local ancestry can be estimated using AIMs or high density SNPs, and both Chen et al. [2013] and Yorgov et al. [2013] compared inference on local ancestry when using the two types of marker sets. Chen et al. found that that the LAMP-LD software, which models the LD of dense SNP sets, outperforms the LAMP method that relies on low-LD AIMs. Yorgov et al. [2013] reported that their local ancestry analysis using LAMP-LD with high-density SNPs produced close to the expected number of ancestry blocks that would be expected for Mexican populations, while the LAMP-LD analysis with a sparse set of AIMs produced too few ancestry blocks. Chen et al. [2013] also compared local ancestry estimates when using phased versus unphased genotypes with the MULTIMIX program, and found that estimates for local ancestry were more reliable when using unphased genotypes. This finding could be attributed to phasing uncertainty in admixed samples that is not accounted for in local ancestry estimation.
