Table 1.
Total variant calls made by each caller, pre-filtering and post-filtering out variants not suitable for validation by Sanger sequencing a
| MJS | MJ | MS | JS | M | J | S | Total | |
|---|---|---|---|---|---|---|---|---|
| All SNVs predicted, n (% of all variants)b |
1,483 (16.1%) |
83 (0.9%) |
462 (5.0%) |
298 (3.2%) |
1,756 (19.0%) |
2,387 (25.9%) |
2,757 (29.9%) |
9,226 |
| SNVs suitable for validation (% of all SNVs suitable for validation)c |
1385 (54.4%) |
16 (0.6%) |
370 (14.5%) |
57 (2.2%) |
279 (11.0%) |
80 (3.1%) |
360 (14.1%) |
2,547 |
| Average number (range) of filtered SNVs per sample |
51.3 |
0.6 |
13.7 |
2.1 |
10.3 |
3.0 |
13.3 |
94.3 |
| (1 to 246) |
(0 to 6) |
(5 to 42) |
(0 to 11) |
(3 to 33) |
(0 to 23) |
(5 to 25) |
(38 to 321) |
|
| Number (%) of SNVs that could not be used for validation | 98 (6.6%) | 67 (80.7%) | 92 (19.9%) | 241 (80.9%) | 1477 (84.1%) | 2307 (96.6%) | 2397 (86.9%) | 6679 (86.9%) |
Abbreviations: J. JointSNVMix2; JS, JointSNVMix2 + SomaticSniper; M, MuTect, MJ, MuTect + JointSNVMix2; MJS, MuTect + JointSNVMix2; + SomaticSniper; MS, MuTect + SomaticSniper; NRAF, non-reference allele frequency; S, SomaticSniper; SNV, single nucleotide variant.
aCall sets are identified as described in Figure 1.
bPredicted variants were filtered on the basis of read depth and NRAF, as described in the text.
c'Suitable for validation’ means evidence for SNV met criteria for validation by Sanger sequencing (tumor NRAF ≥0.2, germline NRAF ≤0.05 and ≥8 reads in both samples.