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 Moore]

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 Moore]

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

[mickeykuo129]

Hi, this looks really helpful!

I am working with cat genome sequencing data and would like to use this tool, but I am a total beginner to bioinformatics (I started learning about a month ago) and just got my own GitHub account today. I am using a Linux command line environment and can write basic bash scripts, but I'm not as familiar with python.

I downloaded the GVF from Ensembl and cloned your repository, but I didn't see any instructions in the README file about the specific function of or correct order for using the different python scripts. If you have any tips or pointers that you don't mind sharing, I would really appreciate it. I am eager to learn how to use and apply this for my project.

Thank you!