I have some basic questions regarding the CNV calling using CNVkit. I have tried to find the CNV caused between normal and tumor samples, but it was not clear which steps should be done respectively.
- For WGS (Somatic) tumor and normal samples, Should I first run the CNVkit batch then CNVkit call ? or "batch" is enough?
- What would be the WGS Germline CNV calling steps?
- How can I find filter the founded CNV, I mean the criteria for cnr or cnn ? ( I mean the significant CNV for the genes).
Thanks a lot.