malemay/delgbs: Detection of deletions and duplications from GBS data

This package was designed to allow the detection of copy number variation (CNV) from standard genotyping-by-sequencing (GBS) data. Developed with populations of fast neutron mutants in mind, it compares the depth of sequencing in discrete genomic windows between individuals, segments the sequencing depth profiles to identify homozygous deletions, hemizygous deletions, and duplications. The functions included in this package provide the utilities needed for going from a set of BAM alignment files to a set of CNVs as well as high-level plotting functions to allow visualizing the output.

install.packages("remotes")
remotes::install_github("malemay/delgbs")