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Table 9 Recalls and precisions of the four callers for non-dbSNPs

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

  

benchmark

Fuwa

Platypus

GATK-UG

GATK-HC

SAMtools

a. NA24149

 non-dbSNPs

SNP

235,880

300,076

473,231

644,589

568,941

543,132

Indel

41,779

104,329

398,110

125,147

158,748

416,411

 non-dbSNPs in benchmark

SNP

235,880

234,135

230,167

235,362

235,506

234,330

Recall (%)

–

99.26

97.58

99.78

99.84

99.34

Precision(%)

–

78.03

48.64

36.51

41.39

43.14

Indel

41,779

32,682

37,472

34,926

38,036

29,766

Recall(%)

–

78.23

89.69

83.60

91.04

71.25

Precision (%)

–

31.33

9.41

27.91

23.96

7.15

b. NA24149

 non-dbSNPs

SNP

235,889

306,323

486,914

659,433

582,136

551,555

Indel

42,960

105,352

412,520

131,903

167,074

437,377

 non-dbSNPs in benchmark

SNP

235,889

233,881

230,076

235,251

235,477

234,184

Recall (%)

–

99.15

97.54

99.73

99.83

99.28

Precision(%)

–

76.35

47.25

35.67

40.45

42.46

Indel

42,960

33,262

38,642

36,128

39,354

30,455

Recall(%)

–

77.43

89.95

84.10

91.61

70.89

Precision (%)

–

31.57

9.37

27.39

23.55

6.96

c. NA24385

 non-dbSNPs

SNP

235,666

337,194

405,643

420,580

335,917

510,292

Indel

43,316

101,414

287,205

111,591

133,827

393,173

 non-dbSNPs in benchmark

SNP

235,666

234,975

216,620

235,010

235,227

234,147

Recall (%)

–

99.71

91.92

99.72

99.81

99.36

Precision(%)

–

69.69

53.40

55.88

70.03

45.88

Indel

43,316

32,730

32,728

36,766

40,921

31,719

Recall(%)

–

75.56

75.56

84.88

94.47

73.23

Precision (%)

–

32.27

11.40

32.95

30.58

8.07

d. NA24631

 non-dbSNPs

SNP

238,105

279,070

339,514

426,948

353,943

344,006

Indel

29,923

108,105

436,409

124,443

160,437

491,021

 non-dbSNPs in benchmark

SNP

238,105

236,336

232,361

237,545

237,664

236,804

Recall (%)

–

99.26

97.59

99.76

99.81

99.45

Precision(%)

–

84.69

68.44

55.64

67.15

68.84

Indel

29,923

22,869

26,652

26,007

28,970

6885

Recall(%)

–

76.43

89.07

86.91

96.82

23.01

Precision (%)

–

21.15

6.11

20.90

18.06

1.40