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

BMC Genomic Data

Table 5 (Software specific quality scores for the scenario “Entire SNP imputation using external HapMap reference”): percentages of SNPs above a quality cut-off of 0.3 for both MaCH-rsq and IMPUTE-info score are provided

Datasets		MaCH Imputation score observing 10% overlapping masked SNPs			IMPUTE2 Imputation score observing 10% overlapping masked SNPs
Data subset name	#SNPs	10%	20%	50%	10%	20%	50%
ALL	9602	*98.29*	*98.72+*	*98.07+*	*99.57+*	*99.57+*	*99.36*
LQ	8472	*98.29*	*98.50*	*98.07*	*99.57*	*99.57*	*99.57+*
NQ	7923	*98.50+*	*98.50*	*97.64*	*99.57*	*99.57*	*99.36*
BQ	6337	96.57	96.57	92.72	*99.14*	*98.93*	97.43
HQ	4658	96.36	96.36	91.65	*98.50*	*98.07*	96.36

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. Note that MaCH-Rsq and IMPUTE-info scores are defined differently and cannot be compared directly.

ISSN: 2730-6844