We then used the WTCCC2 data to compare pre-phasing against a haplotype sampling approach, both of which were implemented in IMPUTE26. Our results again show that pre-phasing can provide comparable accuracy to the existing imputation method, although in this case the pre-phasing results were slightly less accurate (Table 2). Both pre-phasing and haplotype sampling capture LD information in the GWAS data, but the sampling approach also accounts for some of the uncertainty in phasing the GWAS genotypes, which could explain why it is more accurate here.
