BioMed Research International / 2019 / Article / Tab 2

Review Article

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 callerType of core algorithmType of variantType of variant caller

BAYSICMachine learning (ensemble caller)SNVTumor-normal somatic SNV callers
CaVEManJoint genotype analysisSNVTumor-normal somatic SNV callers
deepSNVAllele frequency analysisSNVTumor-normal somatic SNV callers
EBCallAllele frequency analysisSNV, indelTumor-normal somatic SNV callers
FaSD-somaticJoint genotype analysisSNVTumor-normal somatic SNV callers
FreeBayesHaplotype analysisSNV, indelTumor-normal somatic SNV callers
HapMuCHaplotype analysisSNV, indelTumor-normal somatic SNV callers
ISOWNSupervised learningSNVSingle-sample somatic and germline SNV caller
JointSNVMix2Joint genotype analysisSNVTumor-normal somatic SNV callers
LocHapHaplotype analysisSNV, indelTumor-normal somatic SNV callers
LoFreqAllele frequency analysisSNV, indelTumor-normal somatic SNV callers
LoLoPickerAllele frequency analysisSNVTumor-normal somatic SNV callers
MutationSeqMachine learningSNVTumor-normal somatic SNV callers
MuSEMarkov chain modelSNVTumor-normal somatic SNV callers
MuTectAllele frequency analysisSNVTumor-normal somatic SNV callers
OutLyzerNoise level estimationSNVSingle-sample somatic and germline SNV caller
PlatypusHaplotype analysisSNV, indel, svTumor-normal somatic SNV callers
PiscesPoisson model on read countSNV, indelSingle-sample somatic and germline SNV caller
PoreSeqNanopore specificSNV, indelSingle-sample somatic and germline SNV caller
qSNPHeuristic thresholdSNVTumor-normal somatic SNV callers
RADIAHeuristic thresholdSNVTumor-normal somatic SNV callers
SeuratJoint genotype analysisSNV, indel,svTumor-normal somatic SNV callers
SAMtoolsJoint genotype analysisSNV, indelTumor-normal somatic SNV callers
ShimmerHeuristic thresholdSNV, indelTumor-normal somatic SNV callers
SNooPerMachine learningSNV, indelTumor-normal somatic SNV callers
SNVSnifferJoint genotype analysisSNV, indelTumor-normal somatic SNV callers
SOAPsnvHeuristic thresholdSNVTumor-normal somatic SNV callers
SomaticSeqMachine learning (ensemble caller)SNVTumor-normal somatic SNV callers
SomaticSniperJoint genotype analysisSNVTumor-normal somatic SNV callers
StrelkaAllele frequency analysisSNV, indelTumor-normal somatic SNV callers
ShearwaterNoise level estimationSNVSingle-sample somatic and germline SNV caller
SiNVICTPoisson model on read countSNV, indelSingle-sample somatic and germline SNV caller
SNVerAllele frequency analysisSNV, indelSingle-sample somatic and germline SNV caller
SNVMix2Genotype analysisSNVSingle-sample somatic and germline SNV caller
SomVarIUSNoise level estimationSNV, indelSingle-sample somatic and germline SNV caller
SPLINTERNoise level estimationSNV, indelSingle-sample somatic and germline SNV caller
TVCIon Torrent specificSNV, indel, SVTumor-normal somatic SNV callers
VarDictHeuristic thresholdSNV, indel, SVTumor-normal somatic SNV callers
VarScan2Heuristic thresholdSNV, indelTumor-normal somatic SNV callers
VirmidJoint genotype analysisSNVTumor-normal somatic SNV callers

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