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 each individual in the Val Borbera cohort. This highlights that both methods produce SE rates close to zero on many individuals but SHAPEIT2 is generally more accurate.
