export VCF

Open SouzaBB opened this issue 4 years ago • 2 comments

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.

Nov 08 '21 14:11 SouzaBB

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.

Nov 11 '21 08:11 tetedange13

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.)

Feb 22 '22 05:02 etal