Table 2. Raw SV call numbers for Manta and Lumpy are given in the DUP, DEL, INV and BND columns.
The prioritised calls are shown in the last three columns. The Primary priority column corresponds to the number of detected fusions reported previously in the literature. All samples are from small hybrid capture panels except for the MCF7 sample, thus the relatively low numbers of calls per sample.
| Sample | Algorithm | DUP, DEL, INV | BND | Primary priority | Secondary priority | Tertiary priority |
|---|---|---|---|---|---|---|
| HDC134P rep. 1 | Manta | 5 | 0 | 2 | 2 | 0 |
| Lumpy | 43 | 9 | 1 | 0 | 1 | |
| HDC134P rep. 2 | Manta | 2 | 0 | 2 | 0 | 0 |
| Lumpy | 41 | 4 | 1 | 0 | 0 | |
| HDC134P rep. 3 | Manta | 3 | 0 | 2 | 0 | 0 |
| Lumpy | 41 | 2 | 1 | 2 | 1 | |
| HDC140P rep. 1 | Manta | 1 | 1 | 1 | 1 | 0 |
| Lumpy | 48 | 20 | 1 | 2 | 0 | |
| HDC140P rep. 2 | Manta | 1 | 1 | 1 | 1 | 0 |
| Lumpy | 30 | 12 | 1 | 1 | 0 | |
| HDC140P rep. 3 | Manta | 1 | 1 | 1 | 1 | 0 |
| Lumpy | 56 | 9 | 1 | 3 | 0 | |
| HDC141P rep. 1 | Manta | 0 | 2 | 2 | 0 | 0 |
| Lumpy | 24 | 7 | 1 | 0 | 0 | |
| HDC141P rep. 2 | Manta | 0 | 2 | 2 | 0 | 0 |
| Lumpy | 17 | 1 | 1 | 0 | 0 | |
| HDC141P rep. 3 | Manta | 0 | 2 | 2 | 0 | 0 |
| Lumpy | 25 | 6 | 1 | 1 | 1 | |
| MCF7 (WGS) | Manta | 8,239 | 1,990 | 16 | 48 | 2,814 |
| Lumpy | 4,277 | 2,750 | 21 | 38 | 1,683 | |
| RT4 | Manta | 169 | 158 | 1 | 20 | 135 |
| Lumpy | 1,509 | 14,659 | 1 | 302 | 10,300 | |
| PDX model | Manta | 248 | 65 | 5 | 2 | 164 |
| Lumpy | 143 | 862 | 5 | 8 | 292 | |
| Patient sample | Manta | 30 | 51 | 1 | 6 | 37 |
| Lumpy | 1,034 | 3,621 | 1 | 13 | 177 |