Finally, since it is well established that phasing and imputation can be more challenging in individuals with recent African ancestry because of their reduced LD and higher genetic diversity, we evaluated our pre-phasing approach in the WHI GWAS of African Americans. In this comparison pre-phasing was less accurate than MaCH’s analytical approach by the largest (but still small) margin in Table 2, which we interpret as evidence that accounting for phase uncertainty is more important when the haplotypes are harder to estimate.
