Table 5.
Variant call results before and after applying the refinement model
| Suboptimal SA Variant Call Result of DeepVariant | After Apply Refinement Model in Suboptimal SA | ||||||
|---|---|---|---|---|---|---|---|
| Miscall (#) | Accurate Call (#) | MR | Miscall (#) | Accurate Call (#) | MR | ||
| HG001 | Indels | 376,077 | 515,540 | 42.18% | 131,368 | 475,254 | 21.66% |
| SNVs | 543,627 | 3,262,744 | 14.28% | 291,010 | 3,208,803 | 8.32% | |
| Total | 919,704 | 3,778,284 | 19.58% | 422,378 | 3,684,057 | 10.29% | |
| HG002 | Indels | 329,933 | 563,457 | 36.93% | 82,357 | 495,442 | 14.25% |
| SNVs | 447,245 | 3,353,974 | 11.77% | 199,369 | 3,296,591 | 5.70% | |
| Total | 777,178 | 3,917,431 | 16.55% | 281,726 | 3,792,033 | 6.92% | |