Impact of pre-imputation SNP-filtering on genotype imputation results

BMC Genomic Data

Table 4 (Imputation quality of the scenario ”entire SNP imputation using external HapMap reference”): percentages of overlapping masked genotypes imputed with good Hellinger score (≥0.6) are presented

Datasets		MACH Imputation score based on 10% overlapping masked SNPs			IMPUTE2 Imputation score based on 10% overlapping masked SNPs
Data subset name	#SNPs	10%	20%	50%	10%	20%	50%
ALL	9602	*94.36+*	**94+***	*91.63+*	*94.25+*	*93.77+*	*91.66*
LQ	8472	94.33*	93.99*	*91.61*	*94.14*	*93.68*	*91.68+*
NQ	7923	94.27	93.82*	91.33	*94.13*	93.50	91.39
BQ	6337	91.69*	90.76*	85.08	91.20	90.18	84.85
HQ	4658	91.22*	90.2*	83.64*	90.21	88.97	82.42

Datasets of different pre-imputation quality filtering were considered and different percentages of genotypes were masked. Results of the optimal imputation scenarios are described with (⁺). Results of the filtering scenarios which are not significantly inferior compared to the best scenario, are described with Italic-bold faced letters. An asterisk (*) indicates whether MaCH or IMPUTE2 performed significantly better in the corresponding scenario.

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