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Table 8 Rare and novel variants called by each of the four callers from the WGS data of the Ashkenazim Trio and the Chinese sample

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

AF

 

benchmark

Fuwa

Platypus

GATK-UG

GATK-HC

SAMtools

a. NA24149

  ≤ 5%

Count

182,482

179,986

174,392

181,248

181,586

179,514

Recall (%)

–

98.63

95.57

99.32

99.51

98.37

  ≤ 1%

Count

72,585

71,636

69,736

72,098

72,090

71,434

Recall (%)

–

98.69

96.07

99.33

99.32

98.41

  ≤ 0.5%

Count

54,448

53,757

52,379

54,096

54,041

53,603

Recall (%)

–

98.73

96.20

99.35

99.25

98.45

  ≤ 0.1%

Count

32,831

32,473

31,607

32,637

32,567

32,402

Recall (%)

–

98.91

96.27

99.41

99.20

98.69

  = 0%

(novel)

Count

298,984

265,501

285,754

282,165

282,348

211,935

Recall(%)

–

88.80

95.58

94.37

94.44

70.89

b. NA24143

  ≤ 5%

Count

189,494

187,013

180,969

188,308

188,644

186,607

Recall (%)

–

98.69

95.50

99.37

99.55

98.48

  ≤ 1%

Count

74,701

73,773

71,681

74,253

74,215

73,646

Recall (%)

–

98.76

95.96

99.40

99.35

98.59

  ≤ 0.5%

Count

55,428

54,744

53,241

55,104

55,023

54,664

Recall (%)

–

98.77

96.05

99.42

99.27

98.62

  ≤ 0.1%

Count

33,113

32,711

31,816

32,918

32,831

32,705

Recall (%)

–

98.79

96.08

99.41

99.15

98.77

  = 0%

(novel)

Count

304,746

269,764

291,681

288,547

288,978

215,956

Recall(%)

–

88.52

95.71

94.68

94.83

70.86

c. NA24385

  ≤ 5%

Count

187,589

185,929

163,225

186,412

186,909

185,048

Recall (%)

–

99.12

87.01

99.37

99.64

98.65

  ≤ 1%

Count

74,132

73,539

64,827

73,693

73,720

73,241

Recall (%)

–

99.20

87.45

99.41

99.44

98.80

  ≤ 0.5%

Count

55,153

54,748

48,305

54,851

54,811

54,551

Recall (%)

–

99.27

87.58

99.45

99.38

98.91

  ≤ 0.1%

Count

32,722

32,516

28,673

32,547

32,487

32,443

Recall (%)

–

99.37

87.63

99.47

99.28

99.15

  = 0%

(novel)

Count

303,456

267,728

259,920

289,030

294,058

222,433

Recall(%)

–

88.23

85.65

95.25

96.90

73.30

d. NA24631

  ≤ 5%

Count

241,718

239,035

230,265

240,706

241,089

222,774

Recall (%)

–

98.89

95.26

99.58

99.74

92.16

  ≤ 1%

Count

112,774

111,568

108,087

112,284

112,308

104,437

Recall (%)

–

98.93

95.84

99.57

99.59

92.61

  ≤ 0.5%

Count

88,884

87,972

85,370

88,521

88,467

82,493

Recall (%)

–

98.97

96.05

99.59

99.53

92.81

  ≤ 0.1%

Count

47,358

46,889

45,557

47,135

47,045

44,078

Recall (%)

–

99.01

96.20

99.53

99.34

93.07

  = 0%

(novel)

Count

231,303

208,579

220,259

224,747

227,952

66,392

Recall(%)

–

90.18

95.23

97.17

98.55

28.70

  1. AF, allele frequency; novel, the variant is not in gnomAD