Third, we select the lowest-error complementary haplotype pair in each window (i.e., block triplet) and use it to phase the block in the center of the window. This procedure is fairly straightforward, with the only subtleties being that at error SNPs (i.e., proband hets for which both surrogate haplotypes have the same allele), we defer to the surrogate with higher confidence (from step 1), and when transitioning from one block to the next, we choose the orientation of the next complementary haplotype pair that best continues the current surrogate maternal and paternal haplotypes.
