Genotype submissions were assessed for mendelian errors (where possible), missing data rates and Hardy–Weinberg proportions. QC filters were applied as previously described3; to achieve QC1 status a SNP had to have fewer than two mendelian errors, less than 20% missing data and P > 0.001 for Hardy–Weinberg analysis. The consensus data set consists only of SNPs for which QC+ submissions were available from all analysis panels. Where multiple submissions met the QC criteria the submission with the lowest missing data rate was chosen for inclusion in the non-redundant filtered data set. Comparison of the Phase II HapMap with the Affymetrix 500K genotypes has shown approximately 20 SNPs where the reported minor allele is discrepant (referred to as ‘allele-flipping’). Over the entire data set, we expect that 500–2,000 SNPs have this problem and the vast majority will occur in SNPs from Phase I of the project. The Data Coordination Center (DCC) is working to resolve as many of these as possible.
