COKGEN: Identification of Copy Number Variants Using Optimization

COKGEN is an R Package for identification of copy number variants using SNP microarray data. Unlike existing model-based methods that train their models based on common variations, COKGEN uses an explicitly designed objective function that aims to trade-off noise and parsimony using only a few adjustable parameters. These parameters can be configured based on the characteristics of the experimental platform and target application, so that the solution to the optimization problem is the most accurate set of CNV calls. These characteristics make COKGEN particularly useful for identification of rare copy number variants.

COKGEN was developed by Gokhan Yavas, Mehmet Koyuturk, and Tom LaFramboise at Case Western Reserve University.




Development of COKGEN is supported by National Science Foundation Award IIS-0916102.