Table 1 Tools for detecting somatic single nucleotide variants (sSNVs) from next generation sequencing (NGS) data
From: Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers
| Tool | Version | URL | Remark | Datea | Ref. |
|---|---|---|---|---|---|
| EBCall | 2 | https://github.com/friend1ws/EBCall | Uses an empirical Bayesian model to call sSNVs | Mar. 2013 | [14] |
| JointSNVMix | 0.8(b2) | http://compbio.bccrc.ca | Joint analysis of tumor/normal pairs | Jan. 2012 | [9] |
| MuTect | 1.1.4 | http://www.broadinstitute.org/cancer/cga/mutect | Sensitive detection of low allelic-fraction sSNVs | Feb. 2013 | [13] |
| SomaticSniper | 1.0.2 | http://genome.wustl.edu/software/somaticsniper | High computational efficiency | Dec. 2011 | [10] |
| Strelka | 0.4.10.2 | ftp://strelka@ftp.illumina.com/ | Clean outputs through stringent filtering | May 2012 | [11] |
| VarScan 2 | 2.3.5 | http://varscan.sourceforge.net/ | Sensitive detection of high-quality sSNVs | Feb. 2012 | [12] |