modSaRa: a computationally efficient R package for CNV identification

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Abstract

Summary:

Chromosomal copy number variation (CNV) refers to a polymorphism that a DNA segment presents deletion or duplication in the population. The computational algorithms developed to identify this type of variation are usually of high computational complexity. Here we present a user-friendly R package, modSaRa, designed to perform copy number variants identification. The package is developed based on a change-point based method with optimal computational complexity and desirable accuracy. The current version of modSaRa package is a comprehensive tool with integration of preprocessing steps and main CNV calling steps.

Availability and Implementation:

modSaRa is an R package written in R, C ++ and Rcpp and is now freely available for download at http://c2s2.yale.edu/software/modSaRa.

Contact:

heping.zhang@yale.edu

Supplementary information:

Supplementary data are available at Bioinformatics online.

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