Table 5 Comparison of the mean performance of PRED-LD, DIST and SSIMP when the results of the latter two are filtered using (i) the reported coefficient of determination and keeping only the imputed SNPs with reported R² > 0.5, (ii) retaining the same number of imputed SNPs with PRED-LD (ranked in descending order of R² for DIST and SSIMP) and (iii) considering only the common imputed SNPs of PRED-LD across all intersection combinations. The three methods show comparable performance across all metrics except for speed. Execution time in other methods cannot be reduced since the R² can only be calculated after the imputation is performed

From: PRED-LD: efficient imputation of GWAS summary statistics