using ShapeIT (Delaneau, Marchini, & Zagury, 2012) in pre-phasing and IMPUTE2 (Howie, Donnelly, & Marchini, 2009) for genotype imputation. The posterior probability threshold for “best-guess” imputed genotype was 0.9. Genotypic information for this SNP was available for 100% of the sample2. Imputation was done on the plus strand, and the MAF for the C allele (which corresponds to the G allele in CDP, due to strand differences in genotyping and imputation) was 0.41.
