six different isolated villages in the Friuli Venezia Giulia region of northern Italy [30]. The INGI-CARL cohort contains individuals from Carlantino, a small isolated village in the province of Foggia in southern Italy [30]. The CROATIA-Split (Split) cohort contains individuals from the Croatian city of Split [31]. Finally, a large sample from the Ugandan General Population Cohort (GPC) [32], covering residents of 25 villages in south-Western Uganda were analysed. These final two cohorts are not considered to be isolated and hence are useful as control samples of unrelated individuals. Each of these cohorts contain pedigrees of varying sizes (see Table S1) which can be used to evaluate phasing accuracy. The GPC cohort was genotyped using the Illumina Human OMNI 2.5S chip. All the other cohorts were genotyped using either the Illumina HumanHap300 or HumanCNV370 chips.
