Table 1 shows the SE rates for SHAPEIT2, SLRP, Beagle and HAPI-UR when run on the founder individuals of each cohort, both within and outside SLRP IBD segments. SHAPEIT2 consistently produced the most accurate haplotypes of all methods within IBD regions. SHAPEIT2 had a mean SE rate of between 0.14% (ORCADES) and 0.75% (CARL), the next closest method was SLRP with SE rates between 0.28% (GPC) and 1.99% (Split), followed by Beagle with SE rates between 0.30% (GPC) and 4.38% (Split). HAPI-UR had high SE rates ranging between 0.35% (GPC) and 8.30% (Split). The GPC cohort stands out here, as all methods perform very accurately (% SE) which can be explained by the larger sample size of this cohort (2,676 individuals in total) and the much denser chip (Illumina Human OMNI2.5S) used to genotype this cohort. It is interesting that SHAPEIT2 seems to have the highest SE rates on the CARL cohort, which has only the second lowest level of relatedness between founders (Figure 2 (right)). Figure S6 (left) shows the SLRP IBD SE rate against the SHAPEIT2 rate for
