Table 5. State-of-the-art tools for mutation calling.
| Software | Scope | Reference |
|---|---|---|
| Mutect / Mutect 2 | Somatic SNVs + INDELs | 244/176 |
| Strelka / Strelka 2 | Somatic SNVs + INDELs | 245/175 |
| VarScan 2 | Somatic SNVs + INDELs. Germline variants. copy number variants | 152 |
| SomaticSniper | Somatic SNVs | 246 |
| RADIA | Somatic SNVs from DNA and matched RNA | 247 |
| FreeBayes | SNP calling | 248 |
| samtools / bcftools | Basic variant calling | 249 |
| Platypus | SNP calling | 250 |
| CaVEMan | Somatic SNVs | 251 |
| cgpPindel | Somatic INDELs | 252 |
| SvABA | Somatic INDELs | 253 |
| MuSE | Somatic SNVs | 254 |
| SMuFIN | Somatic SNVs + INDELs | 255 |
| GATK | All purpose toolkit. including germline genotyper | 256 |
| NeuSomatic | Deep Learning based somatic SNV detection | 257 |