Whole genome SNP genotype piecemeal imputation

BMC Bioinformatics

Table 5 Accuracy comparisons between the multi-step piecemeal and the usual two/three-step imputation

BaseProgram	Imputation	a c c ₁	a c c ₂	a c c ₃	a c c _π	+
Beagle	8 Holstein BTA 27	71.29 %	74.25 %		74.43 %	0.18 %
FImpute	6 K →50 K →777 K	82.80 %	82.74 %		82.92 %	0.18 %
Beagle	367 Simmental BTA 14	66.00 %	65.51 %		66.59 %	1.08 %
FImpute	6 K →50 K →660 K	68.43 %	68.54 %		68.56 %	0.02 %
Beagle	23 Simmental BTA 14	84.91 %	89.88 %		90.17 %	0.29 %
FImpute	50 K →660 K →Sequence	87.95 %	90.47 %		90.50 %	0.03 %
Beagle	23 Simmental BTA 14	81.19 %		83.94 %	86.26 %	2.32 %
FImpute	6 K →50 K →660K →Sequence	82.23 %		84.58 %	84.67 %	0.09 %

Results are on the Holstein datasets for markers on chromosome 27 and for the Simmental datasets for markers on chromosome 14, respectively. 8 Holstein and 367 Simmental genotyped animals are used in the two-step independent testing (6 K →50 K →HD), with results in columns 4, 6 and 7. The piecemeal imputation uses the selected markers and their associated target marker clusters from the training step. Additional 23 Simmental sequenced and genotyped animals are used in the two/three-step imputation to Sequence (50K →660K →Sequence, 6K →50K →660K →Sequence). All one-step imputation accuracies are included in column 3. The last column labelled with + show the improvements, in bold, of the piecemeal imputation over the two- or three-step imputation

ISSN: 1471-2105