I've seen a few papers use RNA-seq data to detect CNVs. However, it's always using "custom scripts" in my experience. Is there a publicly available tool for performing that analysis?
I found inferCNV, but that is designed for single-cell data which will have a very different profile from bulk RNA-seq and have a lot more replicates.
There is also CONICS:
Yet another option is CaSpER:
Another option: https://github.com/jmonlong/scCNAutils