We developed a new algorithm, CHIAMO, which we applied to simultaneously call the genotypes from all individuals (see Methods and Supplementary Information). Cross-platform comparison showed CHIAMO to outperform BRLMM (the standard Affymetrix algorithm) by having an error rate under 0.2% (Supplementary Table 3), and comparison of 108 duplicate genotypes in our study gave a discordance rate of 0.12%.
