CNV for species comparative genomics

[VaninaTonzo]

Hi all,

I am trying to use CNVpytor to get copy number variation between different non model species. I have one good reference genome of 1 diploid species and WGS of 9 related species.

I am following the instructions but I have a couple of questions:

1. When I merge the CNV calls for all the species I get numbers on the deletion fields > 0, I am not sure how to interpret this table.

2. how to determine the more accurate bin size? I tried 100, 1000 and 10000.
   This is an example with bin size 10000
   

3. Do you have any suggestion about how to get and compare CNV between different species

Thanks in advance for your help,

V