When focusing on the 1000 Genomes February 2012 release, the highest concordance rates were obtained using IMPUTE2 and MaCH, and these two programs performed equally well across the reference panels (Figure 1). Minimal differences were observed between the most closely related panel (YRI+CEU+ASW, concordance = 92.4% with MaCH and 92.3% with IMPUTE2) and the most diverse panel (ALL, concordance = 92.5% with both MaCH and IMPUTE2), despite the large discrepancy in reference sample size. Comparisons using HapMap phase III and the August 2010 release of 1000 Genomes also showed nearly indistinguishable performance for IMPUTE2 and MaCH, both of which outperformed BEAGLE and MaCH-Admix (Figure S3).
