Imputing rare variants in families using a two-stage approach

BMC Proceedings

Table 4 Summary of Imputation Quality by MAF

Imputation Approach	(0,0.01) 4028 SNPs			(0.01,0.05) 1416 SNPs			(0.05,0.4) 1142 SNPs
Imputation Approach	#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

*#SNP_p is the number of SNPs with a MAF greater than 0 for both real and imputed genotypes (varies by method)
^aCombined (m) indicates the 2-stage imputation approach with MAF cutoff m

ISSN: 1753-6561