Table 14

Positive calling rates of the four calling programs under different coverage cutoffs for dbSNPs and non-dbSNPs
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

Yu and Sun

Yu and Sun BMC Bioinformatics 2013 14:274   doi:10.1186/1471-2105-14-274

Open Data