We first assessed gender miscalls based on X chromosome genotypes and allele calls for Y, adjusting gender when appropriate (e.g. miscoding) and dropping samples (e.g. Klinefelter syndrome) or genotypes (e.g. loss of X in cell line) from the X chromosome. We searched the database for duplicate samples using a subset of 5254 SNPs that were independent and had a >99.9% completion rate for genotypes at this QC stage. Duplicates from four families were removed. Data were subsequently checked for Mendelian errors, and 19 families with large numbers of errors were removed from the analysis. In all other cases of Mendelian inheritance errors, the SNPs were set to missing in the family exhibiting the error. The fraction of complete genotypes per individual was required to be ≥95% over the autosomes; 27 samples fell below this criterion. Following this QC step, 4304 genotyped individuals were retained for 1445 pedigrees.
