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Table 3 Computation time1 required to phase 2000 2SNP for the simulated Ne1000 data when using or ignoring pedigree information

From: A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes

 

Number of individuals

With pedigree

Without pedigree

Pedigree 1

2000

 

30 min 34 s

Pedigree 2 NPG3

1000

4 min 3 s

3 min 3 s

Pedigree 2 PG4

2000

39 min 21 s

26 min 58 s

Pedigree 3 NPG3

1000

7 min 56 s

5 min 20 s

Pedigree 3 PG4

1600

18 min 23 s

17 min 11 s

Pedigree 4 NPG3

1000

9 min30 s

50 min 27 s

Pedigree 4 PG4

1510

17 min 4 s

10 min 48 s

Pedigree 5

3000

106 min 37 s

179 min 52 s

Pedigree 6 sires

2578

78 min 22 s

39 min 43 s

Pedigree 6 last 2000

2000

48 min 24 s

321 min 27 s

Pedigree 7 sires

1777

23 min 47 s

22 min 18 s

Pedigree 7 last 2000

2000

54 min 1 s

74 min 15 s

Pedigree 8

879

4 min 14 s

2 min 41 s

  1. 1A 64 bit desktop with an Intel i7 3.07 GHz quad core processor running Linux was used to measure computation time; computation time measured in minutes and seconds includes time required to parse and summarise the data and write out the results; 2using a core length of 100 SNP and a CplusT length of 300 SNP for each dataset; 3NPG indicates that this dataset did not have parents genotyped; 4PG indicates that this dataset had parents genotyped
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Genetics Selection Evolution

ISSN: 1297-9686