Proposal on CNV (Copies Variants Numer) analysis tools

Question

[AIMAR]

Hello everyone, hoping you all doing well. If anyone can recommend a tool for analyzing copy number variants on somatic data, please let me know.

I'm working with CNVkit, but it doesn't provide very clear documentation. So, if anyone can recommend another tool(s), please let me know.

Thanks.

[GenoMax]

but it doesn't provide very clear documentation.

Documentation for CNVkit appears to be extensive https://cnvkit.readthedocs.io/en/stable/quickstart.html . If there is something that is not clear then you can reach out to the developer via issues section on their GitHub site.

[AIMAR]

I've consulted the documentation and reported an issue in the GitHub site but, since there I've no reply. And I've tried to understand and find a solution but nothing that's why I wanna know if there's another tool I can use instead of CNVkit.

Thanks

[mbyvcm]

What do you need to know that is not not captured in the online documentation?

[GenoMax]

CNVkit CNVs call with threshold issues is the question on Biostars, that was also posted to GitHub.

[AIMAR]

Yes, that's the question.

[AIMAR]

Hi, it's about the call threshold cause I've used -0.20,0.20 as threshold and there's no neutral calls there. However by check the log2 values I should have some neutral calls out there. So I'm kind confused and I would like to understand well the analysis.

Thanks

Answer 1

[raphael.B]

DeepSomatic, which is the equivalent of Deepvariat for somatic variant calling, could be a good alternative (Not tested though).

[AIMAR]

Thanks very much