SNPs that are monomorphic in the panel of interest (e.g., YRI+CEU+ASW for African Americans), hence leaving fewer input SNP genotypes and speeding the imputation procedure. For postimputation filtering, SNPs are imputed using all available reference SNPs as input and then those that are monomorphic in the panel of interest are removed. We applied this postimputation filtering strategy to our imputation results. When considering only the 312,474 SNPs that are polymorphic across the reference panels (i.e., SNPs that are polymorphic in the YRI+CEU+ASW panel) out of 475,371 total SNPs on chromosome 22, use of the ALL panel resulted in the highest average r2hat, both overall (Figure S9 for all programs) and across the MAF spectrum (Figure S10 for IMPUTE2 specifically).
