Table 1.
Precision (Prec), Recall (Rec), and F Score of Each Tool for the Synthetic Mosaic Variants Inserted by Bamsurgeon
| 30X Coverage | Samovar |
MuTect2 |
MosaicHunter |
|||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Tumor-Only |
Paired |
Tumor-Only |
Paired |
Trio |
||||||||||||||
| Prec | Rec | F | Prec | Rec | F | Prec | Rec | F | Prec | Rec | F | Prec | Rec | F | Prec | Rec | F | |
| Autosomes | 84.0 | 30.1 | 44.4 | 3.0 | 83.2 | 5.7 | 60.8 | 91.4 | 73.0 | 31.5 | 5.1 | 8.8 | 79.2 | 20.7 | 32.8 | 70.4 | 20.7 | 32.0 |
| Exons | 84.0 | 28.3 | 42.4 | 3.6 | 85.3 | 7.0 | 60.1 | 92.0 | 72.7 | 35.0 | 7.1 | 11.8 | 82.1 | 30.8 | 44.8 | 73.7 | 30.8 | 43.4 |
| Genes | 84.9 | 30.1 | 44.4 | 3.2 | 84.4 | 6.2 | 63.0 | 92.0 | 74.8 | 32.6 | 5.7 | 9.7 | 79.9 | 22.7 | 35.4 | 71.2 | 22.7 | 34.5 |
| Enhancer | 88.5 | 31.0 | 45.9 | 3.9 | 86.7 | 7.5 | 72.9 | 92.3 | 81.4 | 37.8 | 5.9 | 10.1 | 85.5 | 29.5 | 43.8 | 80.2 | 29.5 | 43.1 |
| Promoter | 83.3 | 26.1 | 39.8 | 3.0 | 83.2 | 5.8 | 59.4 | 90.9 | 71.9 | 35.3 | 6.1 | 10.4 | 80.5 | 25.1 | 38.3 | 73.7 | 25.1 | 37.5 |
| Alu | 82.0 | 28.6 | 42.4 | 2.3 | 78.2 | 4.5 | 54.5 | 88.4 | 67.4 | 8.6 | 0.0 | 0.1 | 56.5 | 0.3 | 0.6 | 53.1 | 0.3 | 0.6 |
| RepeatMasker | 84.2 | 29.6 | 43.9 | 2.8 | 81.5 | 5.3 | 58.9 | 90.1 | 71.2 | 20.2 | 0.3 | 0.6 | 72.3 | 1.4 | 2.7 | 61.3 | 1.4 | 2.7 |
| Seg. Dup. | 25.6 | 10.4 | 14.8 | 1.3 | 56.9 | 2.5 | 18.4 | 62.8 | 28.5 | 6.6 | 0.5 | 0.9 | 39.3 | 1.7 | 3.2 | 29.1 | 1.7 | 3.2 |
| 60X coverage | Prec | Rec | F | Prec | Rec | F | Prec | Rec | F | Prec | Rec | F | ||||||
| Autosomes | 84.6 | 43.0 | 57.1 | 3.6 | 76.0 | 7.0 | 32.4 | 15.5 | 20.9 | 46.8 | 27.2 | 34.4 | ||||||
| Exons | 84.3 | 41.8 | 55.9 | 4.7 | 79.6 | 8.8 | 38.5 | 25.3 | 30.5 | 54.0 | 45.5 | 49.4 | ||||||
| Genes | 85.6 | 43.4 | 57.6 | 3.9 | 77.2 | 7.5 | 33.1 | 17.0 | 22.4 | 47.7 | 30.0 | 36.8 | ||||||
| Enhancer | 90.8 | 47.8 | 62.6 | 4.8 | 77.9 | 9.0 | 36.9 | 22.7 | 28.1 | 51.6 | 40.0 | 45.1 | ||||||
| Promoter | 85.4 | 40.7 | 55.2 | 4.0 | 76.8 | 7.6 | 38.5 | 21.1 | 27.3 | 56.4 | 40.5 | 47.2 | ||||||
| Alu | 81.1 | 42.9 | 56.1 | 3.0 | 68.0 | 5.7 | 16.5 | 0.2 | 0.5 | 31.7 | 0.5 | 1.0 | ||||||
| RepeatMasker | 84.2 | 42.2 | 56.2 | 3.4 | 74.1 | 6.4 | 24.7 | 1.0 | 1.9 | 38.3 | 1.8 | 3.4 | ||||||
| Seg. Dup. | 28.0 | 13.1 | 17.8 | 1.6 | 48.5 | 3.1 | 9.8 | 1.5 | 2.6 | 18.5 | 2.7 | 4.7 | ||||||