Table 1

Comparison of SVseq2, SVseq1 and Pindel in simulation.

Coverage

Tool

Findings

True Positive

Accuracy (%)

Sensitivity (%)


3.2×

SVseq2

114

112

98

85

SVseq1

111

108

97

82

Pindel

91

90

99

68


4.2×

SVseq2

113

112

99

85

SVseq1

117

109

93

83

Pindel

91

90

99

68


6.4×

SVseq2

123

120

98

91

SVseq1

128

120

94

91

Pindel

103

102

99

77


Reads of length 100 on chromosome 15 with 132 deletions are simulated. The cutoff value of SVseq2 is 3. The cutoff value is 3 for SVseq1 and Pindel. Number of findings and true positives in each setting are reported.

Zhang et al. BMC Bioinformatics 2012 13(Suppl 6):S6   doi:10.1186/1471-2105-13-S6-S6

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