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Contact the support of the company, as usual when it is about commercial products.
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I can not answer your TCGAbiolinks question, but I can answer your GDC CNV data question.
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Looks like that file is available from Nature: https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-020-2308-7/MediaObjects/41586…
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[SVbyEye](https://github.com/daewoooo/SVbyEye) says it handles duplications and inversions.
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