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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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export VCF #671

Open SouzaBB opened 2 years ago

SouzaBB commented 2 years ago

Hi.. I'm using cnvkit to detect germline exon level CNV's. So, Is there a way to use the export function with cnr file instead of cns files? When exporting VCF file using the cns files, I'm having a vcf with no values but, there's a actual cnv there with the size of just one exon (~250bp).

I'm using cnvkit v0.9.6

Thanks.

tetedange13 commented 2 years ago

Hi @SouzaBB,

Please start by upgrading CNVkit if you can, because v0.9.6 is pretty old and a lot of bug fixes / improvements have been added since => Then tell us if you still got this empty-values VCF

Have a nice day. Felix.

etal commented 2 years ago

You could try the bintest command to get a .cns of exon-level calls, then export vcf that. (If it doesn't work, please let me know. It ought to work, but you might be the first to try it.)