Table 1.

List of tumor-normal somatic SNV callers sorted in alphabetical order. For each variant caller, the types of variants that are reported (column 2), whether single-sample input is allowed (column 3), and a high-level summary of the core algorithm (column 4) are provided. The variant callers and their core algorithms are explained in detail in Section 3.

Variant caller	Type of variant	Single-sample mode	Type of core algorithm
BAYSIC [48]	SNV	No	Machine learning (ensemble caller)
CaVEMan [34]	SNV	No	Joint genotype analysis
deepSNV [38]	SNV	No	Allele frequency analysis
EBCall [37]	SNV, indel	No	Allele frequency analysis
FaSD-somatic [31]	SNV	Yes	Joint genotype analysis
FreeBayes [44]	SNV, indel	Yes	Haplotype analysis
HapMuC [42]	SNV, indel	Yes	Haplotype analysis
JointSNVMix2 [30]	SNV	No	Joint genotype analysis
LocHap [43]	SNV, indel	No	Haplotype analysis
LoFreq [36]	SNV, indel	Yes	Allele frequency analysis
LoLoPicker [39]	SNV	No	Allele frequency analysis
MutationSeq [45]	SNV	No	Machine learning
MuSE [40]	SNV	No	Markov chain model
MuTect [35]	SNV	Yes	Allele frequency analysis
SAMtools [8]	SNV, indel	Yes	Joint genotype analysis
Platypus [41]	SNV, indel, SV	Yes	Haplotype analysis
qSNP [24]	SNV	No	Heuristic threshold
RADIA [26]	SNV	No	Heuristic threshold
Seurat [33]	SNV, indel, SV	No	Joint genotype analysis
Shimmer [25]	SNV, indel	No	Heuristic threshold
SNooPer [47]	SNV, indel	Yes	Machine learning
SNVSniffer [32]	SNV, indel	Yes	Joint genotype analysis
SOAPsnv [27]	SNV	No	Heuristic threshold
SomaticSeq [46]	SNV	No	Machine learning (ensemble caller)
SomaticSniper [28]	SNV	No	Joint genotype analysis
Strelka [17]	SNV, indel	No	Allele frequency analysis
TVC [97]	SNV, indel, SV	Yes	Ion Torrent specific
VarDict [18]	SNV, indel, SV	Yes	Heuristic threshold
VarScan2 [9]	SNV, indel	Yes	Heuristic threshold
Virmid [29]	SNV	No	Joint genotype analysis