Interpretation of WGS copy number plot

[kristianunger]

When running CNVkit in tumor-only mode, the copy number plots look like this:

It looks that the centromeric and partly telomeric regions have a "mirrored" copy number pattern. CNVkit is supposed to mask the repeats regions when building the reference if I am correct, so I would like to request your advice what you think when you see that pattern and if there is anything I could do to avoid the "mirrored" copy number patterns.