Table 2.

Selected representative CNV calling methods

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]