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Variant caller | Type of core algorithm | Type of variant | Type of variant caller |
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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 |
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