How to detect your own CNVs

How to detect copy number variation (CNV) in your own genotype chip data, can be found in a companion paper of the recent Nature publication.
In the previous Nature paper the authors explained their algorithm to be based on k-means and PAM (partitioning around medoid) clustering, but it seems quite different. They call genotypes with DM (which seems to be already obsolete by the BRLMM, see a comparison at Broad and the AFFX whitepaper), then adjust heterocygote ratios by Gaussian mixture clustering, normalize and reduce noise before! merging NspI and StyI arrays. The software is at Genome Science, Tokyo. Yea, yea.