Accounting for CNV in single cell ATAC-seq in cancer sample

Question

[abcoxyzide]

I am interested in the chromatin accessibility of cancer cells, in particular any differences between clones. We plan to perform scATAC-seq (perhaps scRNA-seq as well).

However, I am worried that the copy number alterations may affect the peak calling. This is especially relevant when my interest is in clonal heterogeneity, where I would need to disentangle between an altered copy number VS altered chromatin accessibility.

I've seen an answer for normalizing ChIP-seq data before, which suggested to call CNV from input control data, and remove these regions from analysis. However, I don't think input control is available for scATAC-seq.

My questions are:

1. Is my worry legit?
2. Are there any ways to normalize the ATAC-seq data by copy number?
3. If yes, can it be done by inferred copy number changes from scATAC-seq / scRNA-seq data? I've seen a couple preprints / published articles, but not sure which methods should be used / if they are reliable.

Thanks in advance for any input / discussion.