Imputation of high-density genotypes in the Fleckvieh cattle population

Table 4 Computing time for the imputation of high-density SNP on chromosomes 1, 15 and 25

Number of animals in reference and validation population	Chr	Beagle	MaCH ^a	findhap.f90^b	Minimac ^c
50 / 747	BTA1	2.67 h	1.30 h (0.03 h / 0.30 h / 0.97 h)	0.07 h	0.17 h (0.03 h / 0.07 h / 0.07 h)
	BTA15	1.18 h	0.68 h (0.02 h / 0.14 h / 0.52 h)	0.04 h	0.09 h (0.02 h / 0.04 h / 0.03 h)
	BTA25	0.67 h	0.37 h (0.01 h / 0.08 h / 0.28 h)	0.04 h	0.05 h (0.01 h / 0.02 h / 0.02 h)
100 / 697	BTA1	3.93 h	5.01 h (0.08 h / 1.11 h / 3.82 h)	0.07 h	0.27 h (0.08 h / 0.06 h / 0.13 h)
	BTA15	2.48 h	2.72 h (0.05 h / 0.55 h / 2.12 h)	0.05 h	0.15 h (0.05 h / 0.03 h / 0.07 h)
	BTA25	1.33 h	1.48 h (0.03 h / 0.32 h / 1.13 h)	0.04 h	0.09 h (0.03 h / 0.02 h / 0.04 h)
200 / 597	BTA1	4.49 h	18.92 h (0.20 h / 4.31 h / 14.41 h)	0.07 h	0.48 h (0.20 h / 0.05 h / 0.23 h)
	BTA15	2.87 h	10.06 h (0.11 h / 2.22 h / 7.73 h)	0.05 h	0.27 h (0.11 h / 0.03 h / 0.13 h)
	BTA25	1.38 h	5.76 h (0.06 h / 1.24 h / 4.45 h)	0.04 h	0.14 h (0.06 h / 0.01 h / 0.07 h)
400 / 397	BTA1	3.73 h	81.23 h (0.44 h / 21.97 h / 58.82 h)	0.07 h	1.1 h (0.44 h / 0.03 h / 0.63 h)
	BTA15	2.45 h	40.16 h (0.21 h / 10.52 h / 29.43 h)	0.05 h	0.56 h (0.21 h / 0.02 h / 0.33 h)
	BTA25	1.37 h	28.30 h (0.11 h / 5.98 h / 22.21 h)	0.04 h	0.30 h (0.11 h / 0.01 h / 0.18 h)

The number of imputed SNP was 36 599, 20 145 and 10 981 for chromosomes 1, 15 and 25, respectively. Computing was performed on an Intel Xeon 2.13 Ghz processor.
^a The entire computing time for MaCH can be partitioned into three separate steps (in parentheses): pre-phasing of the reference population with Beagle, inference of tuning parameters based on 200 randomly selected animals of the validation population and actual genotype imputation with MaCH.
^bfindhap.f90 was run exploiting the multi-threading option.
^c The entire computing time for Minimac can be partitioned into three separate steps (in parentheses): pre-phasing of the reference population with Beagle, pre-phasing of the validation population with Beagle and actual genotype imputation with Minimac.

ISSN: 1297-9686