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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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VCF file recommendations #655

Open tea-kostic opened 3 years ago

tea-kostic commented 3 years ago

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 commented 3 years ago

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? https://github.com/etal/cnvkit/issues/601#issuecomment-835861846

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.