Hello,
We currently don’t have a specific threshold recommendation for determining amp/del using relative copy number data, but perhaps the discussion in this thread could be helpful.
And in case you are interested in absolute copy number calls instead of relative to classify CNAs, we currently have data generated by the ABSOLUTE algorithm on the CCLE lines. You can find the file called CCLE_ABSOLUTE_combined_20181227 in the “CCLE 2019” data set on the download page.
Simone
