removed. Related individuals (full siblings, half siblings/avunculars) were not removed from the final datasets. In the HumanHap dataset, 107 individuals were removed because they were duplicates or flagged for removal in the genotyping step, leaving 6,787 subjects. In addition, 8 pairs of individuals were flagged as related. In the OmniExpress dataset, we removed 39 subjects leaving 5,917 IDs and 5 pairs of related subjects. In the Affymetrix dataset, 167 individuals were removed because they were duplicates or were flagged for removal from secondary genotype data cleaning, leaving a total of 8,065 individuals. Across all three datasets, we identified 444 duplicate pairs (406 expected) and thus removed additional 482 individuals from analysis across all three platform families.
