Table 2 The number of inserted “truth” SNPs in each data set and the numbers detected by each caller. The numbers listed in the first row next to “truth” indicate the number of inserted SNPs in the set
From: Comparing the performance of selected variant callers using synthetic data and genome segmentation
Callers | Set_1 Truth:3535 | Set_2 Truth:4322 | Set_3 Truth:7903 | Set_4 Truth:16268 | ||||
|---|---|---|---|---|---|---|---|---|
True positive | False positive | True positive | False positive | True positive | False positive | True positive | False positive | |
FreeBayes | 3379 | 6212 | 4150 | 6533 | 6989 | 5558 | 8762 | 9521 |
VarDict | 3443 | 6988 | 4224 | 6094 | 7366 | 5388 | 12,598 | 4456 |
MuTect | 3303 | 755 | 4081 | 1176 | 7100 | 1098 | 11,708 | 1030 |
Ensemble | 3202 | 199 | 4085 | 278 | 7031 | 135 | 10,666 | 450 |
MuTect2 | 3334 | 384 | 4087 | 966 | 7131 | 817 | 11,876 | 535 |
MuSE | 3447 | 583 | 4197 | 432 | 6952 | 299 | 8941 | 1353 |