Copynumber Pipeline

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

A prerelease version of the paper is available here:

Application Note

Supplement

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

Documentation detailing the pipeline inputs and outputs is also available at this link.

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