available for that individual and takes values on a continuum between 0 and 2, and a hard call imputation, which gives the best integral guess for the number of rare alleles, either 0, 1, or 2. We had available 1,038 BrCa controls, which we labeled “controls,” and 1,672 T2D controls, which we labeled “cases.” SNPs with MAF < 0.025 (calculated using both groups after imputation) or imputation quality R2 < 0.30 (calculated in either group) were removed.
