IMPUTE to the HGDP data of Conrad et al. [2006]. Table VIII tabulates the proportion of markers imputed with r2>0.80 in each population using either MaCH or IMPUTE (in each case, we selected the HapMap reference panel that provided the best imputed genotypes). Overall, the two methods perform similarly. MaCH slightly outperforms IMPUTE in 37 out of 52 populations, slightly underperforms in 13 populations and the two methods are tied in the remaining two populations. Our results are consistent with other published comparisons [Biernacka et al., 2009; Pei et al., 2008], which include detailed comparisons of the performance of MaCH and IMPUTE with each other and with alternative imputation approaches such as BEAGLE and fastPHASE.
