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

BMC Genomic Data

Table 2 Imputation quality of the scenario “Hole-filling without external reference”: percentages of masked genotypes imputed with a Hellinger score ≥0.6 are presented

Datasets		MACHImputation score based on 10% overlapping masked genotypes			IMPUTE2: Imputation score based on 10% overlapping masked genotypes
Data subset name	#SNPs	10%	20%	50%	10%	20%	50%
ALL	9602	93.15*	**92.29+***	87.59*	*92.43*	*91.55*	*86.08+*
LQ	8472	**93.23+***	92.23*	**87.85+***	*92.51+*	*91.56+*	*86.00*
NQ	7923	93.08*	92.09*	87.48*	92.29	*91.36*	85.64
BQ	6337	89.82*	88.24*	79.53*	89.00	87.31	76.89
HQ	4658	89.47*	87.71*	78.56*	88.72	86.95	75.82

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 letters. An asterisk (*) indicates whether MaCH or IMPUTE2 performed significantly better in the corresponding scenario.

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