Table 2 Classification statistics based on different thresholds.
Quality thresholds | “High quality” variants (unconfirmed variants) | “Low quality” variants (unconfirmed variants) | Test #1 “LQ bin identifies unconfirmed variants” | ||
|---|---|---|---|---|---|
Sensitivity (Recall) | Precision | F1-score | |||
DP ≥ 35, AF ≥ 0.352 | 738 (0) | 1018 (5) | 100% | 0.5% | 0.010 |
DP ≥ 30 QUAL ≥ 3013 | 1088 (0) | 668 (5) | 100% | 0.7% | 0.015 |
DP ≥ 2012 | 1549 (1) | 207 (4) | 80.0% | 1.9% | 0.038 |
DP ≥ 20 AF ≥ 0.3 FILTER = PASS QUAL > 3005 | 1357 (0) | 399 (5) | 100% | 1.3% | 0.025 |
DP ≥ 20 AF ≥ 0.2 FILTER = PASS QUAL ≥ 10011 | 1546 (0) | 210 (5) | 100% | 2.4% | 0.047 |
DP ≥ 20 AF ≥ 0.2 | 1547 (0) | 209 (5) | 100% | 2.4% | 0.047 |
DP ≥ 15 AF ≥ 0.25 | 1672 (0) | 84 (5) | 100% | 6.0% | 0.112 |
QUAL ≥ 100 | 1735 (0) | 21 (5) | 100% | 23.8% | 0.385 |
