CNVkit result interpretation

Question

[enes]

Hi, I want to cnv analysis with CNVkit tool to clinical exome panel germline sample.

I used this code:

cnvkit.py batch S58.bam --normal S*.bam --targets my_targets.bed --fasta Homo_sapiens_assembly38.fasta --access access-5kb.hg10.bed --output-reference my_reference.cnn --output-dir results/

When I checked the S58.call.cns file I see that result

Is it make sense? Because I check the 25. row (chr19, cn=0) from UCSC genome browser:

Deletion covers the entire chromosome. How can I interpret this result? I think there is wrong somewhere..

Thank you!

[brunobsouzaa]

You've performed call command on cns files? I would recommend doing it on cnr files. After that, I would filter the file by excluding everything that has cn=2. I also work with germline CNV detection and it works fine for me. I would also suggest you to use ExomeDepth along with cnvkit. This will give you much more reliable results.