CNVkit result interpretation
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!
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You've performed
callcommand oncnsfiles? I would recommend doing it oncnrfiles. After that, I would filter the file by excluding everything that hascn=2. I also work with germline CNV detection and it works fine for me. I would also suggest you to useExomeDepthalong withcnvkit. This will give you much more reliable results.