Table 1 Comparison of the present method with other methods
From: A new approach for detecting low-level mutations in next-generation sequence data
Method | Parts of the read used | Thresholds | Expected haplotype number | False positives | False negatives | Reference |
|---|---|---|---|---|---|---|
CRISP | All | -4; -1,000; -1,000 | 20 | 5 | 0 | [15] |
All | -4; -1,000; -1,000 | 50 | 4 | 0 | ||
SPLINTER | First 12 bp | -1.301 | 20 | 2 | 12 | [17] |
First 70 bp | -6.6 | 20 | 123 | 0 | ||
First 12 bp | -1.301 | 50 | 2 | 12 | ||
First 70 bp | -6.6 | 50 | 634 | 0 | ||
MAQ | All | 60 | 20 | 848 | 3 | [31] |
All | 60 | 50 | 1,130 | 3 | ||
All | 200 | 20 | 0 | 6 | ||
All | 200 | 50 | 1 | 8 | ||
VarScan | All | 1e-10 | NA | 190 | 0 | [30] |
Poisson | All | 10 | NA | 0 | 0 | Our method |
Fisher exact | All | 10 | NA | 0 | 0 | Our method |
Empirical | All | 10 | NA | 0 | 0 | Our method |