Table 3.
SVs detected by SViCT and compared tools in the Horizon reference data set. Lumpy2 predicted an incorrect fusion partner and Pindel is not designed to predict translocations
| Variant Type | Chr | Gene | Variant | SViCT | Lumpy2 | GridSS | Socrates | Delly2 | Pindel |
|---|---|---|---|---|---|---|---|---|---|
| Deletion | 7 | EGFR | E746_A750delELREA | Yes | No | No | No | No | Yes |
| Insertion | 7 | EGFR | V769_D770insASV | Yes | N/A | No | No | No | Yes |
| Fusion | 4:6 | ROS1 | SLC34A2/ROS1 | Yes | Yes | No | Yes | Yes | N/A |
| Fusion | 10 | RET | CCDC6/RET | Yes | Incorrect | No | Yes | Yes | N/A |
| Total Calls Run 1 | 3026 | 9967 | 1980 | 1904 | 4878 | 94 869 | |||
| Total Calls Run 2 | 2105 | 8881 | 3463 | 1900 | 8972 | 75 582 |
Only SViCT was able to predict all four SVs. All tools found/missed the same SVs between the two replicates.