Table 2.
List of tumor-normal somatic SNV callers and single-sample somatic and germline SNV callers sorted in alphabetical order.
| Variant caller | Type of core algorithm | Type of variant | Type of variant caller |
|---|---|---|---|
| BAYSIC | Machine learning (ensemble caller) | SNV | Tumor-normal somatic SNV callers |
| CaVEMan | Joint genotype analysis | SNV | Tumor-normal somatic SNV callers |
| deepSNV | Allele frequency analysis | SNV | Tumor-normal somatic SNV callers |
| EBCall | Allele frequency analysis | SNV, indel | Tumor-normal somatic SNV callers |
| FaSD-somatic | Joint genotype analysis | SNV | Tumor-normal somatic SNV callers |
| FreeBayes | Haplotype analysis | SNV, indel | Tumor-normal somatic SNV callers |
| HapMuC | Haplotype analysis | SNV, indel | Tumor-normal somatic SNV callers |
| ISOWN | Supervised learning | SNV | Single-sample somatic and germline SNV caller |
| JointSNVMix2 | Joint genotype analysis | SNV | Tumor-normal somatic SNV callers |
| LocHap | Haplotype analysis | SNV, indel | Tumor-normal somatic SNV callers |
| LoFreq | Allele frequency analysis | SNV, indel | Tumor-normal somatic SNV callers |
| LoLoPicker | Allele frequency analysis | SNV | Tumor-normal somatic SNV callers |
| MutationSeq | Machine learning | SNV | Tumor-normal somatic SNV callers |
| MuSE | Markov chain model | SNV | Tumor-normal somatic SNV callers |
| MuTect | Allele frequency analysis | SNV | Tumor-normal somatic SNV callers |
| OutLyzer | Noise level estimation | SNV | Single-sample somatic and germline SNV caller |
| Platypus | Haplotype analysis | SNV, indel, sv | Tumor-normal somatic SNV callers |
| Pisces | Poisson model on read count | SNV, indel | Single-sample somatic and germline SNV caller |
| PoreSeq | Nanopore specific | SNV, indel | Single-sample somatic and germline SNV caller |
| qSNP | Heuristic threshold | SNV | Tumor-normal somatic SNV callers |
| RADIA | Heuristic threshold | SNV | Tumor-normal somatic SNV callers |
| Seurat | Joint genotype analysis | SNV, indel,sv | Tumor-normal somatic SNV callers |
| SAMtools | Joint genotype analysis | SNV, indel | Tumor-normal somatic SNV callers |
| Shimmer | Heuristic threshold | SNV, indel | Tumor-normal somatic SNV callers |
| SNooPer | Machine learning | SNV, indel | Tumor-normal somatic SNV callers |
| SNVSniffer | Joint genotype analysis | SNV, indel | Tumor-normal somatic SNV callers |
| SOAPsnv | Heuristic threshold | SNV | Tumor-normal somatic SNV callers |
| SomaticSeq | Machine learning (ensemble caller) | SNV | Tumor-normal somatic SNV callers |
| SomaticSniper | Joint genotype analysis | SNV | Tumor-normal somatic SNV callers |
| Strelka | Allele frequency analysis | SNV, indel | Tumor-normal somatic SNV callers |
| Shearwater | Noise level estimation | SNV | Single-sample somatic and germline SNV caller |
| SiNVICT | Poisson model on read count | SNV, indel | Single-sample somatic and germline SNV caller |
| SNVer | Allele frequency analysis | SNV, indel | Single-sample somatic and germline SNV caller |
| SNVMix2 | Genotype analysis | SNV | Single-sample somatic and germline SNV caller |
| SomVarIUS | Noise level estimation | SNV, indel | Single-sample somatic and germline SNV caller |
| SPLINTER | Noise level estimation | SNV, indel | Single-sample somatic and germline SNV caller |
| TVC | Ion Torrent specific | SNV, indel, SV | Tumor-normal somatic SNV callers |
| VarDict | Heuristic threshold | SNV, indel, SV | Tumor-normal somatic SNV callers |
| VarScan2 | Heuristic threshold | SNV, indel | Tumor-normal somatic SNV callers |
| Virmid | Joint genotype analysis | SNV | Tumor-normal somatic SNV callers |