Given a tumor-only sample, I am looking to perform copy number analysis and generate plots and tables. Could you please recommend tools that would best meet these requirements? Thank you!

Do you have WES or WGS? If you have WES, this may be difficult without any panel of normals. If you have a bunch of tumor samples and they have their CNAs all in different places, you could maybe try to use the collective as a kind of "PON", in the hope that the average is close to "normal". For WES, the commonly used tool is CNVkit. Don't know about tumor-only, but it works alright with decent-quality tumor-normal data. For visualization you can use cnaplotr. For WGS, i think ASCAT should be helpful, but I don't have much experience with that. If you have a suspicion of where a CNA is occurring, you can even look at it in IGV and might be able to see it.

Thank you, Thomas. I have 5 tumor-only WES samples and have been trying using mutect2 and CNVkit for variant calling and copy number analysis.

Hi Sean, let me know how is your process going. I'm working with WES/WGS tumor only analysis, and now I'm curious about how sarek works with cnvkit in CNA WES tumor only analysis.