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Table 2 The performance comparison on a simulated data set for g e=0.04

From: Joint haplotype assembly and genotype calling via sequential Monte Carlo algorithm

 

ParticleHap

HapCUT

ReFHap

 

n

c

ImpGeAc

ReconRate

Time(s)

ReconRate

Time(s)

ReconRate

Time(s)

100

4

0.6254

0.9785

0.02

0.9598

0.66

0.9497

0.11

 

6

0.6252

0.9794

0.02

0.9570

0.84

0.9481

0.25

 

8

0.5977

0.9792

0.03

0.9590

1.01

0.9524

0.56

 

10

0.5737

0.9780

0.03

0.9582

1.17

0.9517

1.23

200

4

0.5935

0.9779

0.07

0.9594

1.78

0.9499

0.26

 

6

0.5977

0.9783

0.08

0.9597

2.26

0.9518

0.88

 

8

0.5840

0.9757

0.09

0.9596

2.71

0.9524

2.56

 

10

0.5758

0.9777

0.11

0.9593

3.13

0.9528

5.80

300

4

0.6013

0.9715

0.17

0.9591

3.39

0.9493

0.53

 

6

0.5848

0.9720

0.20

0.9596

4.34

0.9511

2.12

 

8

0.5842

0.9695

0.22

0.9598

5.14

0.9525

6.35

 

10

0.5671

0.9703

0.24

0.9599

5.90

0.9537

14.68

  1. A comparison of reconstruction rate(ReconRate) and running time(Time) for different haplotype assembly algorithms, ParticleHap, HapCUT and ReFHap, on the simulated data for g e=0.04. For ParticleHap, the improvement rates of genotyping accuracy (ImpGeAc) are also reported
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BMC Bioinformatics

ISSN: 1471-2105

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