compared, many of these discrepancies could be attributed to miscalled genotypes in the parents, i.e. the LRP result could often be correct. Ten offspring had more than 3 discrepancies. Three of these 10 are siblings and they account for over 50% (468/845) of the total genotype discrepancies. One sib has IBS ≥ 1 with each of the other two sibs, who shared both haplotypes in this region, but the sharing does not result from sharing one haplotype for the entire target region, but rather sharing the paternal haplotype for part of the region and the maternal haplotype for another part with overlap. This complication contributed directly to the phasing mistake and we expect that future adjustments to the algorithm will reduce such errors (Supplementary Note online).
