Is it possible to regenotype a VCF using giraffe?

vgteam / vg

tools for working with genome variation graphs

https://biostars.org/tag/vg/

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Is it possible to regenotype a VCF using giraffe? #4330

Open rickymagner opened 2 months ago

rickymagner commented 2 months ago

Hi, I posted this question on Biostars here a few months ago but never received a response.

In short, is it possible to both:

Use giraffe to create a GAM from reads against a VCF-augmented graph
Regenotype the same VCF using the read evidence from vg call -v?

The README says that the indices/files created in the giraffe workflow cannot be used when running vg call -v . Is it correct to conclude that there is no possible way to use both of these tools together?

Thanks

jeizenga commented 2 months ago

Yes, it is possible, but we don't currently have a workflow for it in vg autoindex (previously noted here: https://github.com/vgteam/vg/issues/3974), so you would need to use the manual indexing pipeline:vg construct -a, vg gbwt -v, vg gbwt --gbz-format, vg index -j, vg minimizer -d.