We used the GAIN dataset to compare a well-benchmarked imputation method (MaCH) against a related method that uses pre-phasing (minimac). Encouragingly, both methods produced similar accuracy when applied to a common reference panel of 60 CEU individuals (Table 2). In fact, our pre-phasing strategy generated slightly better results despite ignoring the uncertainty in the estimated GWAS haplotypes, possibly because pre-phasing captures joint LD information that is not used by the analytical phasing/imputation framework of methods like MaCH and IMPUTE1.
