Table 1. A list of commonly used open-source variant callers and their usage possibilities.

Variant caller	Tumor-only mode	Variant type detection	References
CaVEMan	NO	SNV	Jones et al. (2016)
DeepSNV	NO	SNV	Gerstung et al. (2012)
DeepVariant	YES	SNV, Indel	Poplin et al. (2018)
EBCall	NO	SNV, Indel	Shiraishi et al. (2013)
FreeBayes	YES	SNV, Indel	Garrison & Marth (2012)
HapMuc	YES	SNV, Indel	Usuyama et al. (2014)
LocHap	NO	SNV, Indel	Sengupta et al. (2016)
LoFreq	YES	SNV, Indel	Wilm et al. (2012)
MuSE	NO	SNV	Fan et al. (2016)
Mutect	YES	SNV	Cibulskis et al. (2013)
Mutect2	YES	SNV, Indel	Benjamin et al. (2019)
Octopus	YES	SNV, Indel	Cooke, Wedge & Lunter (2018)
Platypus	YES	SNV, Indel	Rimmer et al. (2014)
SAMtools	YES	SNV, Indel	Li et al. (2009)
SomaticSniper	NO	SNV	Larson et al. (2012)
Strelka2	NO	SNV, Indel	Kim et al. (2018)
UMI-VarCal	YES	SNV	Sater et al. (2020)
VarDict	YES	SNV, Indel	Lai et al. (2016)
VarScan2	YES	SNV, Indel	Koboldt et al. (2012)