We consider extensions of the pre-phasing approach in the Supplementary Material, including an exploration of multiple imputation approaches and an example of how imputation accuracy can be improved by pre-phasing with other haplotyping engines like SHAPEIT17. We also note that when genotypes from family members are available, it may be particularly attractive to use our imputation software with haplotypes informed by transmission patterns in pedigrees, where the best phasing tool may depend on family structure.
