Tool | Built-in parallelisation enabled? | Simulated samples (single-chromosome BAM files), minutes | Clinical samples (full BAM files), minutes | NA12878 (full BAM file), minutes | Joint calling, minutes |
---|---|---|---|---|---|
Manta | Auto | 2.3(1.7) | 76.5(21.0) | 70 | \(397^{\dagger }\) |
CNVnator | Auto | 1.4(0.7) | 22.0(0.8) | 32 | \(133^{\dagger }\) |
CNVpytor | Yes | 3.6(2.1) | 15.3(0.5) | 27 | \(121^{\dagger }\) |
Control-FREEC | Yes | 2.3(1.2) | 31.2(7.2) | 36 | \(182^{\dagger }\) |
ConanVarvar | Yes | 1.7(0.9) | 21.5(0.6) | 32 | 63 |
ConanVarvar | No | 1.8(0.8) | 22.5(1.3) | 33 | 131 |