SNV
| Tools | Pros | Cons | Used in Logan |
| Mutect2 | Part of GATK best practices | | x |
| Strelka | Fast | Paired only | x |
| Muse | Fast | Paired only, can't be parallelized | x |
| Lofreq | Low frequency variants | Slow,Paired only | x |
| Vardict | Fast | Lower accuracy | x |
| Varscan | Fast | Lower accuracy | x |
| Octopus | Accurate | Slow,High memory | x |
| Deepsomatic | Relatively fast | Trained on human data | x |
Structural Variants
| Tools | Pros | Cons | Approach | Used in Logan |
| Manta | Accurate, fast | | graph-based | x |
| SVABA | Deletion detection | | local assembly+ multiple alignment | x |
| GRIDSS | Provides blacklist | Slow, part of HMFtools pipeline | Break end assembly (discordant +split) | x |
Manta, GridSS, and SvABA are based on read-pairs, split-reads, and local-assemblies.
References Joe et al
Copy Number
| Tools | Pros | Cons | Used in Logan |
| Purple | Complete workflow | Doesn't support mm10, requires SV,SNV calls as well | x |
| Sequenza | Purity/Ploidy | | x |
| FREEC | Fast | No Purity/Ploidy Estimatation | x |
| ASCAT | Fast, Purity/Ploidy | | x |
| CNVkit | Fast | No Purity/Ploidy Estimatation | x |
| PureCN | Tumor only | Needs Panel of Normals on Sequencing | |
Germline
| Tools | Pros | Cons | Used in Logan |
| Deepvariant | Fast, most accurate | Model trained on human genomes (May not support mm10) | x |