Hi guys, I am newbie in CNVkit, I have read documentation but I confused about my results. I want to analyse for clinical exome panel.

I created reference cnn with this code:

cnvkit.py reference -o Flat_Reference.cnn -f hg38_ref_genome.fasta -t my_targets.target.bed -a my_targets.antitarget.bed

When I create Flat_Reference.cnn file like that, I take approximately 61k copy number variant from cnr file. Is it make sense? I'm probably making a mistake somewhere but I couldn't find the mistake?

Could anyone help me about it? Thanks.