All of the methods have lower SE rates than when run on just the founders of the pedigrees (Table 1) but the improvement for SHAPEIT2 is most striking. We find that SHAPEIT2 achieves between 0.059% (Korcula) and 0.241% (CARL) SE rate on individuals within pedigrees. SLRP achieves a very high yield in most cohorts (% except in Split and GPC) for individuals within pedigrees and improved accuracy within the IBD regions it detects. Both Beagle and HAPI-UR (3×) are also more accurate in this setting as well but do not obtain the same gains as SHAPEIT2.
