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Table 4 Summary of Imputation Quality by MAF

From: Imputing rare variants in families using a two-stage approach

Imputation Approach (0,0.01)
4028 SNPs
(0.01,0.05)
1416 SNPs
(0.05,0.4)
1142 SNPs
#SNPp* Mean Var #SNPp* Mean Var #SNPp* Mean Var
IQS
Impute2 3023 0.840 0.097 1164 0.772 0.126 761 0.899 0.048
Merlin 4028 0.348 0.132 1416 0.437 0.041 1142 0.404 0.006
Combined (0.01)a 4028 0.350 0.133 1416 0.965 0.017 1142 0.992 0.004
Combined (0.05) a 4028 0.349 0.133 1416 0.443 0.041 1142 0.992 0.004
Correlation
Impute2 3023 0.918 0.048 1164 0.981 0.006 761 0.999 0.00004
Merlin 4028 0.512 0.195 1416 0.663 0.064 1142 0.687 0.007
Combined (0.01) a 4028 0.514 0.196 1416 0.975 0.010 1142 0.994 0.003
Combined (0.05) a 4028 0.513 0.196 1416 0.669 0.063 1142 0.993 0.003
  1. *#SNPp is the number of SNPs with a MAF greater than 0 for both real and imputed genotypes (varies by method)
  2. aCombined (m) indicates the 2-stage imputation approach with MAF cutoff m