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 |