Table 1.
Bioinformatic methods available for single nucleotide variant calling. Tools marked with an asterisk (*) are suitable for both whole genome sequencing (WGS) and whole exome sequencing (WES) data analysis.
| Name | Published | Cited in 2018 | Control Needed | InDel detection | Contamination Correction | Trained on Cancer Data | Environment | Ref |
|---|---|---|---|---|---|---|---|---|
| Varscan2 | 2012 | 2229 | + | + | − | + | Java, Perl, R, Galaxy | [21] |
| MuTect2 * | 2013 | 2005 | + | − | + | + | Java, R | [20] |
| FreeBayes | 2012 | 1121 | − | + | − | + | C, C++, Galaxy | [24] |
| Strelka * | 2012 | 759 | + | + | − | + | C++, Perl | [23] |
| Platypus * | 2014 | 462 | − | + | − | + | C, Cython, Python | [36] |
| SomaticSniper * | 2012 | 373 | + | − | − | + | C, Galaxy | [22] |
| LoFreq * | 2012 | 349 | − | + | + | + | Python | [37] |
| VarDict * | 2016 | 171 | − | + | − | + | Perl | [38] |
| JointSNVMix * | 2012 | 160 | + | − | − | + | C, C++, Python, Galaxy | [39] |
| MutationSeq * | 2012 | 108 | + | − | − | + | C++, Python | [40] |
| EBCall * | 2013 | 85 | + | + | − | + | C++, Perl, R, Shell | [41] |
| MuSE * | 2016 | 65 | + | − | + | + | C, C++ | [42] |
| RADIA | 2014 | 53 | + | − | + | + | Python | [43] |
| Virmid | 2013 | 49 | + | − | + | + | Java | [44] |
| deepSNV * | 2014 | 47 | + | − | − | + | R | [45] |
| Shimmer * | 2013 | 45 | + | − | + | + | C, Perl, R | [46] |
| qSNP * | 2013 | 40 | + | − | + | − | Java | [47] |
| BAYSIC | 2014 | 39 | + | − | − | + | R | [48] |
| SomaticSeq * | 2015 | 38 | + | + | − | + | Python, R | [49] |
| CaVEMan * | 2016 | 31 | + | − | + | + | C | [50] |
| SNooPer * | 2016 | 26 | − | + | + | + | Perl | [51] |
| SNVSniffer * | 2016 | 17 | − | + | − | + | C++ | [52] |
| HapMuC | 2014 | 15 | − | + | − | + | C++, Python, Ruby | [53] |
| FaSD-somatic | 2014 | 13 | − | − | − | + | C, C++ | [54] |
| LocHap * | 2016 | 8 | + | + | + | + | g++ complier, GNU Make | [55] |
| LoLoPicker * | 2017 | 6 | + | − | + | + | Python | [56] |