Copynumber Pipeline

The Copynumber Pipeline operates on Affymetrix SNP6 array data.  It calls genotypes and relative copynumber levels.

You can find detailed documentation at the following link:

http://www.broadinstitute.org/software/copynumber

You can run or download the software from the Broad GenePattern server (requires free GenePattern registration)

http://genepattern.broadinstitute.org/gp/pages/index.jsf?lsid=CopyNumberInferencePipeline