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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...