Comparing the GVF file & VCF file

Question

[Alireza]

Hi guys

I checked some organisms (like dogs) that Ensembl has reported germline variants in VCF & GVF format.

But some variants in the GVF file do not exist in the VCF file!

Why does this happen?

[barslmn]

Searching always an option.

https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format

[Alireza]

This link is about the GVCF format. my question is about the GVF format. I think these two formats are different.

[Ben_Ensembl]

Here is information about the GVF variant format: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-8-r88

[GenoMax]

But some variants in the GVF file do not exist in the VCF file!

You may want to email Ensembl help desk and ask. Provide examples to them. GVF seems to be only used by Ensembl.

[Ben_Ensembl]

Thanks GenoMax - yes, please do send details of the missing variants to the Ensembl Helpdesk and we will do our best to help you from there.

[Alireza]

Thanks for your response.

Also, I wrote an easy script to convert GVF to VCF.

I think it works well.

https://github.com/Test-Blu/GVF2VCF_Convertor_TestBlu