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Proposal on CNV (Copies Variants Numer) analysis tools

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.

number_variant somatic_data help copy
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written by AIMAR • 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

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written by AIMAR • AIMAR

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

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written by mbyvcm mbyvcm

Yes, that's the question.

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written by AIMAR • 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

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written by AIMAR • AIMAR

1 answer

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

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written by raphael.B • raphael.B

Thanks very much

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written by AIMAR • AIMAR

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