Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery

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