Table 1 Selected tools for the performance analysis of CNV detection tools using WES data
From: An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
Tool name | ADTEx | CONTRA | cn.MOPS | ExomeCNV | VarScan 2 |
|---|---|---|---|---|---|
Chara- Cteristics | |||||
Control set required | Yes | Yes | No | Yes | No |
Prog. Language | Python, S/R | Python, R | R | R | Java |
Input format | BAM, BED | BAM, SAM, BED | BAM, Read count matrices | BAM, Pileup, GTF | BAM, Pileup |
Segmentation Algorithm | HMM | CBS | CBS | CBS | NAa |
OS | GNU, Linux | Linux, Mac OS | Linux, Mac OS, windows | Linux, Mac OS, windows | Linux, Mac OS, windows |
Methodology characteristic | DWTc for de-noising, use BAFd | Base-level log-ratio | Bayesian approach for de-noising | Statistical test for analyzing BAF data | CMDSb for generating read counts |
Year | 2014 | 2012 | 2012 | 2011 | 2012 |
URL | https://secure.genome.ucla.edu/index.php/ExomeCNV_User_Guide |