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Table 4 Overall computing run time in minutes for the different imputation scenarios 1,2

From: Accuracy of genome-wide imputation in Braford and Hereford beef cattle

Panel FImpute Beagle
NE-P NNE-P NE-NP NNE-NP NE-NP NNE-NP
  Imputation to the 50K SNP panel 3
3K 2 6 41 39 2280 2131
6K 3 7 46 45 828 772
8K 3 7 45 45 808 656
15K 3 9 48 48 328 317
20K 3 7 37 42 708 622
  Imputation to the 777K SNP panel 4,5
3K 16 (17,24) - 4 (5,8) - 64 (224,41) -
6K 17 (23,24) - 4 (19,21) - 49 (238,33) -
8K 17 (23,24) - 3 (20,23) - 45 (177,34) -
15K 15 (24,23) - 8 (20,23) - 40 (127,42) -
20K 17 (23,23) - 9 (20,23) - 44 (161,42) -
50K 3 - 11 - 29 -
90iK 17 - 11 - 25 -
90tK 17 - 10 - 33 -
  1. 1Run time based on 10 parallel jobs with computer with 4*6-core processors (Intel Xeon X5690 @ 3.47GHz) and 128 Gigabytes of memory in OS x86-64 GNU/Linux;
  2. 2Scenarios for imputation. (NE-P) - using Nellore genotypes in the reference population and considering pedigree information; (NNE-P) - not using Nellore genotypes in the reference population and considering pedigree information; (NE-NP) - using Nellore genotypes in the reference population and not using pedigree information; (NNE-NP) - not using Nellore genotypes in the reference population and not using pedigree information;
  3. 32,735 or 2,647 (not using Nellore genotypes) animals in the reference population and 963 animals in the imputation population;
  4. 4Values outside the brackets refer to the one-step imputation. The reference and imputation population were formed by 175 and 43 animals, respectively;
  5. 5Values inside the brackets refer to the two-step imputation. The reference population were formed by 3,567 in the imputation from low density panel to the 50K SNP panel and 175 animals in the imputation from the 50K SNP panel to the 777K SNP panel. The imputation population was formed by 43 animals.