After filtering based on various quality and yield criteria, 289,658 autosomal markers and 8,411 markers on chromosome X were used. Excluding those with no parent listed in the genealogy database or with less than 98% genotyping yield, 38,167 individuals, a majority typed with Illumia HumanHap300/CNV370 bead chips (Supplementary Information), were processed. For these individuals, 97.8% of the heterozygous genotypes were long range phased, 99.8% of these had parental origin determined. Overall, 3,841,331,873 heterozygous genotypes, 97.7% of those called, had parental origin assigned. The data includes 2,879 typed trios. To empirically evaluate the accuracy of our method, a run was performed with the data of parents in these trios removed when determining parental origin. For 231,585,437 heterozygous genotypes in the probands/offspring, parental origin was determined both by our method and by the trio data directly, with 500,330 discrepancies, an error rate of 500,300/231,585,437 = 0.22%. Since the trios tested have passed heritability checks in pre-processing, the error rate for individuals with fewer than two parents genotyped is probably higher. Still, the overall error rate is likely below 0.4% (Supplementary Information).
