The software calculates a confidence score for each sample-SNP data point and those beyond a fixed threshold have their genotype set to missing. Samples with low quality scans are repeated. Post-production metrics are used to eliminate low quality samples and SNPs from the Genotyping Center data release, using project-specific thresholds. These metrics vary among platforms and projects, and may include call rate, allele frequency-plate associations, Hardy-Weinberg deviations, duplicate discordance of HapMap controls and sex differences in SNP metrics. More details of Genotyping Center QC are provided in Supporting Information.
