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. 2022 Jan 3;2:800380. doi: 10.3389/fragi.2021.800380

TABLE 1.

A selected list of tools for somatic mutation calling.

Tool Reference Sequencing type Detectable mutation type Optimized for non-cancer data Built-in genotyper Matched control required Base-quality-aware in genotyper Joint analysis of multiple samples
Strelka Saunders et al. (2012) bulk DNA Shared No Yes Yes No Yes, with matched control
VarScan2 Koboldt et al. (2012) bulk DNA Shared No Yes Yes No Yes, with matched control
JointSNVMix Roth et al. (2012) bulk DNA Shared No Yes Yes Yes Yes, with matched control
MuTect Cibulskis et al. (2013) bulk DNA Shared No a Yes Yes a Yes Yes, with matched control
MosaicHunter Huang et al. (2014) Huang et al. (2017) bulk DNA Shared Yes Yes No Yes Yes, with matched control or parents
SomVarIUS Smith et al. (2016) bulk DNA Shared No Yes No Yes No
EM-mosaic Hsieh et al. (2020) bulk DNA Shared Yes Yes No No No
MosaicForecast Dou et al. (2020) bulk DNA Shared Yes No No NA No
Shearwater Gerstung et al. (2014) bulk DNA, ultra-deep Shared No Yes Yes No No
RareVar Hao et al. (2017) bulk DNA, ultra-deep Shared No Yes No No No
RePlow Kim et al. (2019) bulk DNA, ultra-deep Shared Yes Yes No Yes No
Monovar Zafar et al. (2016) single-cell DNA Shared and private No Yes Yes No Yes, with other single cells
SCcaller Dong et al. (2017) single-cell DNA Shared and private Yes Yes Yes Yes No
LiRA Bohrson et al. (2019) single-cell DNA Shared and private Yes No Yes NA No
Conbase Hard et al. (2019) single-cell DNA Shared Yes Yes Yes No Yes, with other single cells
SCAN-SNV Luquette et al. (2019) single-cell DNA Shared and private Yes No Yes NA No
single-cell MosaicHunter Huang et al. (2020) single-cell DNA Shared Yes Yes No Yes Yes, with bulk or other single cells
RNA-MuTect Yizhak et al. (2019) bulk RNA Shared Yes Yes Yes Yes Yes, with matched DNA
SCmut Vu et al. (2019) single-cell RNA Shared No No Yes NA Yes, with matched DNA
a

Later versions of MuTect, with dramatic improvement from the method described in the original paper, allow somatic mutation calling in non-cancer samples and without matched control.