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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see exomeCopy.

Copy number variant detection from exome sequencing read depth

Bioconductor version: Release (3.18)

Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

Author: Michael Love

Maintainer: Michael Love <michaelisaiahlove at>

Citation (from within R, enter citation("exomeCopy")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Copy number variant detection in exome sequencing data PDF R Script
Reference Manual PDF


biocViews CopyNumberVariation, Genetics, Sequencing, Software
Version 1.48.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL (>= 2)
Depends R (>= 3.5.0), IRanges(>= 2.5.27), GenomicRanges(>= 1.23.16), Rsamtools
Imports stats4, methods, GenomeInfoDb
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Suggests Biostrings
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Depends On Me
Imports Me cn.mops, CNVPanelizer, contiBAIT
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