Individuals in pedigrees obviously share large amounts of their genome IBD. Algorithms that have the ability to exploit IBD sharing in distantly related individuals may also work well on explicitly related individuals. Hence, we also evaluated the accuracy of SHAPEIT2, SLRP, HAPI-UR and Beagle applied to the full cohorts described here, with the full extended pedigrees included. We ran each of the methods using no information regarding relatedness of samples. We calculated SE for each method on the haplotypes of any individual in a pedigree larger than a mother-father-child pedigree, using the Merlin haplotypes as truth.
