Table 3.
Computational methods available for copy number variation estimation from whole exome sequencing data. Tools marked with an asterisk are suitable for both WGS and WES data analysis.
| Name | Published | Control Needed | Contamination Correction | GC-Content Correction | Trained on Cancer Data | Cited in 2018 | Environment | Ref. |
|---|---|---|---|---|---|---|---|---|
| Varscan2 | 2012 | + | − | − | + | 2229 | Java, Perl, R, Galaxy | [21] |
| CNVnator | 2011 | + | − | + | − | 767 | C++ | [86] |
| CNV-Seq | 2009 | + | − | − | − | 463 | Perl, R | [87] |
| CoNIFER | 2012 | − | + | − | − | 378 | Python | [88] |
| Control-FREEC * | 2012 | − | + | + | + | 342 | C, C++, R | [89] |
| ExomeCNV | 2011 | + | + | − | + | 338 | R | [90] |
| XHMM | 2012 | − | + | + | + | 322 | C++ | [91] |
| ExomeDepth | 2012 | + | − | + | − | 264 | R | [92] |
| cn.MOPS | 2012 | − | + | + | − | 249 | R | [93] |
| Cnvkit * | 2016 | + | + | + | + | 219 | Python, Galaxy | [94] |
| CONTRA | 2012 | − | − | + | − | 194 | Python, R | [95] |
| Sequenza * | 2015 | + | − | + | + | 167 | Python, R | [96] |
| EXCAVATOR | 2013 | + | + | + | + | 155 | Perl | [97] |
| CODEX | 2015 | − | + | + | + | 72 | R | [98] |
| ADTEx | 2014 | + | + | − | + | 57 | Python, R | [99] |
| Seqgene | 2011 | + | − | − | + | 43 | R | [100] |
| FishingCNV | 2013 | − | − | − | − | 41 | Java, R | [101] |
| HMZDelFinder | 2017 | − | − | − | − | 33 | R | [102] |
| ExoCNVTest | 2012 | + | − | − | − | 27 | Java, R | [103] |
| CLAMMS | 2016 | − | − | + | − | 23 | C | [104] |
| falcon | 2015 | + | + | − | + | 22 | C | [105] |
| saasCNV * | 2015 | + | + | − | + | 17 | R | [106] |
| WISExome | 2017 | − | − | − | − | 1 | C, C++ | [107] |