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@HeejunJang I ran into similar problems. See my suggested solution here: https://github.com/etal/cnvkit/issues/765#issuecomment-1363743810

Unfortunately the parameters used for the filtering are currently hard-coded in this file (L3-L5): https://github.com/etal/cnvkit/blob/0f827c0a360cbcac5e26eed830727abf1a066722/cnvlib/params.py#L1 I would also be in favour of being able to change the default parameter settings....

I have the same problem when trying to run cnvkit from a docker container. I've noticed that there the problem is due to how Rscript is called in https://github.com/etal/cnvkit/blob/master/cnvlib/segmentation/__init__.py. If...

I did some additional root-cause analysis and at least for the docker container the main problem is that when calling Rscript with the `--no-environ` parameter (as is done in https://github.com/etal/cnvkit/blob/master/cnvlib/segmentation/__init__.py#L161),...

@ashleyacevedo @tskir @chim9 I ran into the same issue and was (I think) able to determine the cause of the issue. Before sending the data to DNAcopy for smoothing and...

Cnvkit performs some internal filtering (based on gc, log2, spread and depth=0) of bins that might skew the CNV calling results. My understanding is that the cnvkit smoothing fails (which...