As reviewed elsewhere [2], there are several software packages with different algorithms available for genotype imputation. We compared imputation results using four widely used programs: IMPUTE2 version 2.2.2 [17], BEAGLE version 3.3 [24], MaCH version 1.0.16.c [5], and MaCH-Admix (beta version 2.0.150). MaCH and BEAGLE were previously shown to outperform other software programs not evaluated here [25], while MaCH-Admix and IMPUTE2 represent recent software advancements that create tailored reference panels for individual study subjects. It is important to note that the current version of MaCH-Admix is a prerelease. MaCH-Admix is being developed to extend the capabilities and shorten the computing run time of MaCH 1.0, by incorporating a novel piecewise reference selection method that creates the tailored reference panels. All of the available details on the Mach-Admix beta version can be found at http://www.sph.umich.edu/csg/yli/MaCH-Admix/.
