PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population
Fig 3
Parental origin assignment process.
For a given quasi-founder, we denote his/her haplotypes by A and B, and (by convention) the first is paternal and the second is maternal. At each SNV, we calculate a 2×2 matrix of kinships (Step 1) between each of the proband’s parents and each subject in the A and B IBD cliques. Using these, we generate a parental haplotype separation measure m (Step 2). If m≈1, A and B are already correctly ordered; if m≈-1, they should be swapped. If the majority of the SNVs agree on the same swapping (indicated by a sample separation M sufficiently close to 1 in Step 3), we assign paternal origin and reorder A and B accordingly (Step 4).