BMC Bioinformatics

Table 14 Positive calling rates 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	0.734	0.888	0.902	0.892
≥ 4X	0.735	0.867	0.882	0.868
≥ 5X	0.704	0.841	0.874	0.876
≥ 6X	0.723	0.819	0.867	0.870
≥ 7X	0.696	0.808	0.817	0.862
≥ 8X	0.747	0.796	0.864	0.852
≥ 9X	0.727	0.782	0.813	0.849
≥ 10X	0.769	0.780	0.862	0.828
B. non-dbSNPs
Coverage cutoffs	SOAPsnp	Atlas-SNP2	GATK-UGT	SAMtools
≥ 3X	0.438	0.863	0.628	0.628
≥ 4X	0.545	0.896	0.713	0.615
≥ 5X	0.602	0.875	0.708	0.610
≥ 6X	0.641	0.873	0.691	0.627
≥ 7X	0.620	0.852	0.730	0.672
≥ 8X	0.594	0.827	0.736	0.674
≥ 9X	0.615	0.824	0.745	0.690
≥ 10X	0.559	0.818	0.674	0.667

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ISSN: 1471-2105

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