how can I analyse gender spesific CNV analysis with CNVkit?

Question

[enes]

Hi,

Recently I am working on CNV analysis with CNVkit tool.

For now, I analyse CNV without use gender parameter. So if my sample come from a woman, my results include loss of Y chromosome. This is not logical.

As far as I know we can use gender parameter while plotting CNV diagram.

Like that:

• cnvkit.py diagram -s sample.cns --gender x or y (woman=x, man = y)

but I want to add this parameter at the beginning of the CNVkit pipeline. Is there any way to do that?

Also I confuse about the weight column. what if weight value is great and log2 value is close to zero (for example 0.2) or vise versa? How can I interpret that situation?

The last question is about diagram plot: Some fields are represented as soft blue/red and some fields are looks like really dark red/blue. How should I interpret that? I guess soft ones are not reliable and dark ones are reliable results. Probably this feature come from log2 ratio but if someone give me more details about that I will be glad to learn that.

Thanks.