Table 2. Compute resources used by the SV callers.
| Software | Dataset | Threads per job | Wall-clock/CPU times* (HH:MM) | Peak mem. (GiB) | Output |
|---|---|---|---|---|---|
| Manta | Cell lines | 24 | 01:45/14:31 | 5.3 | 94 MiB |
| Benchmark | 24 | 00:49/05:42 | 2.8 | 225 MiB | |
| DELLY | Cell lines | 2 | 19:23/25:47 66:03/85:20 |
3.6 | 13 MiB |
| Benchmark | 1 | 00:54/00:49 09:07/08:35 |
0.9 | 28 MiB | |
| LUMPY | Cell lines | 1 | 13:40/20:55 | 24.4 | 5.9 GiB |
| Benchmark | 1 | 00:29/00:45 | 5.7 | <1 MiB | |
| GRIDSS | Cell lines | 24 | 29:31/214:13 | 44.4 | 73 GiB |
| Benchmark | 24 | 08:24/26:04 | 38.5 | 342 MiB |
Notes:
*
Timings per sample or per job are averaged using median over ten WGS (paired) samples.
DELLY calls per sample were summed over jobs of distinct SV types.
LUMPY is mostly single-threaded except its I/O related code, which results in CPU time > wall-clock time.