Third, we analyze the set of identified probable IBD matches for consistency, truncating or eliminating matches until we reach a consistent set. For any pair of overlapping probable IBD matches between the proband and potential surrogate parents 1 and 2, the implied shared haplotypes can be (a) consistent with the proband sharing the same haplotype with both surrogates 1 and 2, (b) consistent with the proband sharing one of its haploytpes with surrogate 1 and other with surrogate 2, or (c) inconsistent with both of these possibilities. We first identify pairs of overlapping probable IBD matches in which scenario (c) occurs; for these pairs, we assume the longer match is correct and trim the shorter match until consistency under either scenario (a) or (b) is achieved. If any match drops below 3cM after during this trimming procedure, we discard the match. At the end of the procedure, all remaining pairs of trimmed matches are consistent. We then perform a final check for global consistency of implied phase orientations among all matches, i.e., we reduce (if necessary) to a subset of
