rCNV: Detect Copy Number Variants from SNP Data

Functions in this package import filtered VCF files of SNP data and generate datasets to detect copy number variants, visualize them, and perform downstream analyses (e.g. environmental association analyses).

Main WGS functions

allele.info.WGS3

Duplication/deletion detection using a negative-binomial depth model; no GC correction.

allele.info.WGS.GCcor

Same framework with per-SNP GC-bias correction via SNP-centred windows.

See also

Useful links:

• https://piyalkarum.github.io/rCNV/

• https://cran.r-project.org/package=rCNV

• Report bugs at https://github.com/piyalkarum/rCNV/issues

Author

Piyal Karunarathne piyalkarumail@yahoo.com