In the realistic scenario we simulated genotyping errors based on a confusion matrix (Table S2) from a previous study [42], that was estimated by comparing genotypes called on both an Affymetrix Axiom chip and a Illumina Omni 2.5S chip on 1000 Genomes individuals. There were many cases where founders were missing in practice. We also removed the 91 ungenotyped founders leaving 108 genotyped founders and a total of 314 individuals in pedigrees. Finally these extended pedigrees were merged with the 607 female chromosome X data (and the remaining 33 pseudo-autosomal males not in a pedigree) to create a cohort of 954 individuals containing 314 individuals in pedigrees and 640 unrelated individuals. We created 10 versions of this simulated dataset. In the ideal scenario we do not add any genotyping error and do not remove founders (leaving all 199 founders in the data giving us a data set with 1045 individuals (405 within a pedigree).
