Table 2 The distribution by the ClinVar category of genetic variants according to three different variant callers.
Clinical significance | GATK HC | VarScan | MuTect2 |
|---|---|---|---|
Association | 70 (0.14%) | 67 (0.16%) | 0 (0.00%) |
Benign | 31,816 (64.96%) | 27,175 (64.50%) | 1079 (61.20%) |
Drug_response | 1504 (3.07%) | 1354 (3.21%) | 19 (1.08%) |
Likely_benign | 8697 (17.76%) | 7658 (18.18%) | 404 (22.92%) |
Likely_pathogenic | 134 (0.27%) | 129 (0.31%) | 16 (0.91%) |
Not_provided | 3534 (7.22%) | 2860 (6.79%) | 78 (4.42%) |
Other | 276 (0.56%) | 258 (0.61%) | 5 (0.28%) |
Pathogenic | 405 (0.83%) | 364 (0.86%) | 21 (1.19%) |
Protective | 306 (0.62%) | 285 (0.68%) | 7 (0.40%) |
Risk_factor | 753 (1.54%) | 674 (1.60%) | 10 (0.57%) |
Uncertain_significance | 1483 (3.03%) | 1305 (3.10%) | 124 (7.03%) |
Sum | 48,978 (100.00%) | 42,129 (100.00%) | 1763 (100.00%) |
