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Table 1 Performance and runtimes on SMASH synthetic benchmark

From: SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations

Caller

SNP calling (%)

Indel calling (%)

Time(s)

 

Recall

Precision

F-score

Recall

Precision

F-score

 

Venter

 

SNVSniffer(M1)

98.5

97.1

97.8

68.9

83.0

75.3

133

SNVSniffer(M2)

98.3

97.4

97.8

69.0

83.7

75.6

320

SNVSniffer(M3)

97.9

98.5

98.2

70.4

83.6

76.4

1331

SAMtools

98.3

97.1

97.7

63.7

69.5

66.5

2046

GATK

98.1

99.1

98.6

76.2

86.2

80.9

2538

FaSD

98.0

97.5

97.7

−

−

−

2005

Contaminated venter

 

SNVSniffer(M1)

98.0

97.4

97.7

69.0

84.0

75.8

119

SNVSniffer(M2)

97.8

97.8

97.8

68.7

84.5

75.8

336

SNVSniffer(M3)

97.3

98.7

98.0

69.7

84.3

76.3

1387

SAMtools

98.1

97.3

97.7

62.7

72.1

67.1

2046

GATK

97.9

96.8

97.3

75.8

86.4

80.8

2803

FaSD

97.4

97.5

97.4

−

−

−

2070

  1. Best results are highlighted in boldface