Table 15

Sensitivities 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 0.980 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

Yu and Sun

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

Open Data