Our recent research suggests that the SHAPEIT2 method is currently the most accurate method for phasing sets of known genotypes. The method uses a similar HMM to approaches such as Impute2 [6] and MaCH. A key feature of the method is that the hidden Markov model calculations are linear in the number of haplotypes being estimated, whereas Impute2 and MaCH scale quadratically. The method uses a unique approach that represents the space of all possible haplotypes consistent with an individual’s genotype data in a graphical model. A pair of haplotypes consistent with an individuals genotypes are represented as a pair of paths through this graph, with constraints to ensure consistency that are easy to apply due to the model structure. For this reason SHAPEIT2 is among the most computationally tractable methods [7, 8].
