VCF file recommendations

[tea-kostic]

Hi,

We want to use CNVkit for CNV calling on somatic data. What kind of VCF file should we use for best results? Should it contain germline or somatic variants or both? Is there any specific caller that you recommend? Or should we use a VCF with known SNPs?

Thanks in advance,
Tea

[tetedange13]

Hi @tea-kostic,

I am not very aware of that, but CNVkit documentation being a bit obscure on this topic is a known problem
=> I think comment from this issue might answer some of your questions? #601 (comment)

Also you should know that CNVkit takes VCF as input only for call step and for visualisation with scatter

Hope this helps.
Have a nice day.
Felix.

[etal]

Answered by pointing to existing threads; underlying VCF-docs gap. Closing as answered — please reopen, or open a new issue, if a concrete problem remains. Related ongoing work: #697.

For general usage questions, we now use GitHub Discussions (Q&A): https://github.com/etal/cnvkit/discussions