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what did you find so far ?
I have found autoCNV, inCNV, and ClassifyCNV. The second one is for exomic CNVs only, and the third one does not run on Windows, but it might be the best one. I will start with the first one: autoCNV. What is not clear yet, is whether the software can handle thousands of CNVs or if you have to submit one at a time instead (as in the web interface).
If someone knows of a better option, please let me know.