Table 4 Comparison of TT-Mars and VaPoR. The two methods agree on most calls and can analyze a similar number of calls across short-read callsets. On the long read callset, TT-Mars evaluates 39,187 additional variants, the majority of which are under 100 bases
From: TT-Mars: structural variants assessment based on haplotype-resolved assemblies
| Â | Â | TT-Mars | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Wham | LUMPY | ||||||
| Â | Â | TP | FP | NA | Sum | TP | FP | NA | Sum |
| Â | TP | 1503 | 98 | 76 | 1677 | 2614 | 288 | 282 | 3184 |
VaPoR | FP | 42 | 108 | 29 | 179 | 163 | 434 | 276 | 873 |
| Â | NA | 267 | 149 | 80 | 496 | 345 | 515 | 1370 | 2230 |
| Â | Sum | 1812 | 355 | 185 | 2352 | 3122 | 1237 | 1928 | 6287 |
| Â | Â | HG00171 | HG00096 | ||||||
| Â | Â | DELLY | pbsv | ||||||
| Â | Â | TP | FP | NA | Sum | TP | FP | NA | Sum |
| Â | TP | 5211 | 405 | 480 | 6096 | 42,268 | 8694 | 3531 | 54,493 |
VaPoR | FP | 1009 | 627 | 581 | 2217 | 12,243 | 1320 | 870 | 14,433 |
| Â | NA | 2343 | 581 | 991 | 3915 | 37,646 | 5942 | 2765 | 46,353 |
| Â | Sum | 8563 | 1613 | 2052 | 12,228 | 92,157 | 15,956 | 7166 | 115,279 |
| Â | Â | HG03009 | HG00096 | ||||||