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 want to add this parameter at the beginning of the CNVkit pipeline.

Is there any way to do that?

Thanks.