the remaining samples. We also investigated two other calling algorithms: Illumnus65 and GenoSNP66. All three algorithms were >99% concordant in their calling for 91% of the SNPs on the array. However, manual inspection of a sample of the SNPs with discrepancies indicated that the calls from GenCall were almost invariably superior (generally, because Illumnus or GenoSNP attempted to call SNPs that clustered poorly). Therefore, only the genotypes called by GenCall have been used in the analyses reported here.
