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Table 1 Haplotype phasing accuracy and timing results for one data set.

From: Haplotype association analyses in resources of mixed structure using Monte Carlo testing

   

Missing data rates (%)

   

0

5

10

15

Data

nloci

Phasing type

accuracy

time(s)

accuracy

time (s)

accuracy

time (s)

accuracy

time (s)

CC

5

new*

0.87

1.49

0.85

1.50

0.82

1.94

0.80

2.95

  

HAPLORE‡

0.87

1.75

0.85

2.09

0.82

1.74

0.80

2.4

  

GCHap†

0.87

1.16

0.85

1.28

0.82

1.66

0.80

1.44

 

10

new

0.62

5.94

0.57

10.13

0.53

15.54

0.49

30.21

  

HAPLORE

0.61

20.44

0.56

32.0

0.52

42.73

0.49

56.51

  

GCHap

0.57

2.56

0.53

4.44

0.49

5.19

0.46

7.53

 

15

new

0.36

42.74

0.33

122.48

0.28

316.55

0.26

1260.62

  

HAPLORE

0.36

90.38

0.32

147.25

0.27

167.37

0.21

302.84

  

GCHap

0.30

4.84

0.27

8.17

0.23

11.36

0.22

17.86

TRIO

5

new

0.98

1.53

0.95

1.72

0.92

2.19

0.90

2.49

  

HAPLORE

0.98

1.47

0.95

1.50

0.92

1.17

0.90

1.47

  

GCHap

0.88

1.15

0.85

1.38

0.82

1.54

0.80

1.60

 

10

new

0.95

2.81

0.89

4.45

0.84

6.93

0.77

13.54

  

HAPLORE

0.95

4.48

0.89

7.39

0.84

10.99

0.77

35.09

  

GCHap

0.59

3.36

0.55

6.53

0.51

7.44

0.47

10.69

 

15

new

0.92

4.52

0.81

8.15

0.73

15.13

0.65

107.28

  

HAPLORE

0.90

12.50

0.80

56.25

-

-

-

-

  

GCHap

0.36

7.63

0.31

11.45

0.27

16.55

0.24

29.08

ASP

5

new

0.99

1.05

0.98

1.61

0.96

1.59

0.95

2.00

  

HAPLORE

0.99

0.61

0.98

0.74

0.96

0.60

0.95

0.67

  

GCHap

0.89

0.98

0.86

1.35

0.84

1.40

0.81

1.43

 

10

new

0.97

2.22

0.95

2.47

0.92

3.30

0.89

3.53

  

HAPLORE

0.97

2.06

0.95

2.53

0.92

3.82

0.89

4.34

  

GCHap

0.60

2.49

0.56

3.74

0.53

5.17

0.48

6.34

 

15

new

0.93

2.99

0.91

3.64

0.85

4.5

0.80

7.90

  

HAPLORE

0.91

3.61

0.89

32.64

-

-

-

-

  

GCHap

0.37

5.31

0.31

7.55

0.28

9.66

0.24

15.59

LP1

5

new

0.99

2.04

0.98

1.88

0.98

1.96

0.97

2.02

  

HAPLORE

-

-

-

-

-

-

-

-

  

GCHap

0.87

1.60

0.86

1.64

0.85

1.69

0.85

1.82

 

10

new

0.98

3.45

0.97

3.80

0.96

3.94

0.95

5.27

  

HAPLORE

-

-

-

-

-

-

-

-

  

GCHap

0.63

4.90

0.61

6.46

0.59

7.00

0.59

6.54

 

15

new

0.96

6.76

0.95

8.23

0.93

10.85

0.92

54.92

  

HAPLORE

-

-

-

-

-

-

-

-

  

GCHap

0.45

8.17

0.42

9.29

0.40

10.72

0.39

15.35

  1. *new pedigree-informed phasing algorithm
  2. ‡HAPLORE (pedigree-informed)
  3. † GCHap (pedigree naïve)
  4. CC (Case Control): 500 cases, 500 controls = 1000 individuals (1000 genotyped)
  5. TRIO (both parents and one offspring): 500 trios = 1500 total individuals (1500 genotyped)
  6. ASP (Affected Sib Pairs and parents): 250 ASPs = 1000 total individuals (1000 genotyped)
  7. LP1 (Large Pedigree) = 5 generational pedigree ~5800 total individuals (~1500 genotyped)
  8. - program failed.