We used the RefinedIBD program103 to call segments of identical-by-descent (IBD) sharing of length ≥ 2 cM on the autosomes using passing SNVs with MAF > 5%. All 53,831 samples were included in this analysis, and we used genotype data phased with Eagle281. As IBD logarithm of odds (LOD) scores are often deflated in populations with strong founding bottlenecks, such as the Amish, we used a LOD score threshold of 1.0 instead of the default 3.0. To account for possible phasing and genotyping errors, we filled gaps between IBD segments for the same pair of individuals if the gap had a length of at most 0.5 cM and at most one discordant genotype. As a result of the lower LOD threshold, regions with a low variant density can have an excess of apparent IBD segments. We therefore identified regions with highly elevated levels of detected IBD using a previously described procedure104 and removed any IBD segments that fell wholly within these regions.
