Identified CNVs only on one chromosome

[Zhaslan Akhmetov]

Dear Tobias Rausch,

I am running the germline CNV calling command from the GitHub tutorial. I have all the necessary files, but Delly is only identifying CNVs on the first chromosome and not on the others. Is there a way to modify the command to detect CNVs across all chromosomes?

Thank you, 

Best Regards,

Zhaslan