BMC Bioinformatics

Table 15 Sensitivities of the four calling programs under different coverage cutoffs for dbSNPs and non-dbSNPs

From: Comparing a few SNP calling algorithms using low-coverage sequencing data

A. dbSNPs
Coverage cutoffs	SOAPsnp	Atlas-SNP2	GATK-UGT	SAMtools
≥ 3X	0.980	0.868	0.958	0.883
≥ 4X	0.960	0.960	0.938	0.858
≥ 5X	0.950	0.967	0.925	0.883
≥ 6X	0.940	0.950	0.910	0.870
≥ 7X	0.941	0.941	0.894	0.882
≥ 8X	0.937	0.937	0.886	0.873
≥ 9X	0.914	0.971	0.871	0.886
≥ 10X	0.923	0.985	0.862	0.815
B. non-dbSNPs
Coverage cutoffs	SOAPsnp	Atlas-SNP2	GATK-UGT	SAMtools
≥ 3X	0.912	0.546	0.837	0.570
≥ 4X	0.968	0.915	0.926	0.628
≥ 5X	0.959	0.946	0.919	0.676
≥ 6X	0.952	1.000	0.903	0.677
≥ 7X	0.942	1.000	0.885	0.750
≥ 8X	0.932	0.977	0.886	0.705
≥ 9X	0.930	0.977	0.884	0.674
≥ 10X	0.917	1.000	0.861	0.667

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ISSN: 1471-2105

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