BMC Bioinformatics

Table 1 Comparison of SVseq2, SVseq1 and Pindel in simulation.

From: An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data

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.

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ISSN: 1471-2105

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