In motivating our new imputation methodology, we pointed out that modeling the study individuals independently, rather than jointly, sacrifices phasing accuracy at typed SNPs; this led us to propose a hybrid approach that models the study haplotypes jointly at typed SNPs but independently at untyped SNPs. We made the latter choice partly to improve efficiency – it is fast to impute untyped alleles independently for different haplotypes, which allows us to use all of the information in large reference panels – but also because of the intuition that there is little to be gained from jointly modeling the study sample at untyped SNPs.
