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Table 2 Comparison of four variant callers on whole-genome sequencing data

From: A study on fast calling variants from next-generation sequencing data using decision tree

  

Whole genome

  

Fuwa

Platypus

GATK-UG

GATK-HC

SAMtools

SNPs

3,820,377

3,271,282

4,441,130

4,034,309

3,959,135

Ti/tv

 

2.03

2.13

1.84

1.94

2.01

Axiom

GT concordance (%)

99.32

98.29

97.3

98.52

99

Sensitivity (%)

96.81

94.34

97.41

97.16

96.88

Mono rate (%)

0.04

0.13

0.22

0.11

0.07

Fosmid

Recall (%)

93.5

90.7

95.03

94.56

93.79

GIAB

Recall (%)

98.41

89.34

98.65

98.44

97.89

Precision (%)

99.26

99.69

97.72

98.79

99.47

Indels

649,387

575,350

711,045

884,204

765,800

In-frame fraction

 

0.47

0.47

0.46

0.51

0.45

Fosmid

Recall (%)

68.04

75.69

64.31

72.25

60.59

GIAB

Recall (%)

87.48

69.49

89.74

94.7

80.98

Precision (%)

95.93

78.49

95.59

94.08

92.32

Runtime (real time, min)

127

233

1058

2545

1546

  1. Ti/tv, transition/transversion rate; GT concordance, concordance of genotypes at Axiom-called loci; Sensitivity, ratio of non-reference calls at Axiom-called loci; Mono rate, fraction of monomorphic Axiom sites that are called as variants; In-frame fraction, fraction of indels (limited to coding regions) whose length are integer multiples of 3; Runtime, CPU minutes needed to process the input bam file; Recall = TP/(TP + FN); Precision = TP/(TP + FP); TP true positive, FN false negative, FP false positive
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BMC Bioinformatics

ISSN: 1471-2105

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