CopyMap is based on a hidden Markov Model (HMM) and predicts the location of CNVs and their allele frequencies using data from a set of CGH experiments. Each hybridization experiment is treated as one realization of the same Markov process, where the hidden states represent the presence or absence of a CNV and the transition probabilities are dependent on its population frequency. We apply a variation of Baum's algorithm to estimate these transition probabilities and the likelihood of each individual to carry a given CNV variant, combining information from all hybridization experiments.
The algorithm is implemented in a program controlled by a command line interface.
The current version is 0.813.
If you use CopyMap please e-mail email@example.com or fill out the registration form. The software and files can be downloaded here. To unpack the file use tar -xvf COPYMAP.tar.gz, then follow the instructions in the manual.