CNVkit interpretation: copy number calculation with the correspondence to the unknown ploidy

Question

[rbioinfo]

Hello,

I aim to detect the number of copies of a particular gene in a cell line from Illumina WGS data. To do so, I use CNVkit and hg38 as a reference genome. However, when I plot the diagrams from cnvkit and by examination of the .bam files directly in the IGV browser I see different coverage from chromosome to chromosome. It seems to me that the ploidy of my cells might be different from diploid (or for at least some of the chromosomes) but I do not have information about ploidy in these cells.

My questions are:

1. How can I interpret the diagrams, meaning, do I have a ploidy different from a diploid?
2. If the ploidy from chromosome to chromosome varies, how It will affect the number of copies of my gene of interest reported by cnvkit?

cnvkit was called within sarek pipeline with default parameters from nf-core

Thank you