daynefiler/mcCNV: Call copy number variants from whole exome/whole genome sequencing data

The package provides a framework for performing depth-based copy number variation estimation. The package is intended to be used with whole- exome sequencing data generated with multiplexed capture (all exomes captured in a single pooled step). The package provides functionality for counting depth over provided intervals, then computes the maximum likelihood copy number based on the negative binomial distribution (adapted from the 'sSeq' algorithm, <doi:10.1093/bioinformatics/btt143>). Additional functionality is provided to simulate read-depth data, helpful for defining sequencing depth requirements and selecting prior values.

install.packages("remotes")
remotes::install_github("daynefiler/mcCNV")