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Table 2 Selected representative CNV calling methods

From: Comparative study of whole exome sequencing-based copy number variation detection tools

Tools

Language

Input format

Methodology

Installation tutorial

Reference

CoNIFER

python

BAM/RPKM、bed、RPKM

Principal Component Analysis

http://conifer.sourceforge.net/index.html

Krumm. et al.(2012) [17]

exomeCopy

R

BAM、bed、Grange

A hidden Markov model which uses positional covariates

http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html

Love. et al.(2011) [18]

CNVkit

python

BAM、bed、cnn

Principal Component Analysis

https://cnvkit.readthedocs.io/en/stable/

Eric. et al.(2016) [19]

cn.MOPS

R

BAM、bed、Grange

Bayesian approach

http://www.bioinf.jku.at/software/cnmops/cnmops.html

Klambauer. et al.(2012) [20]