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9 weeks ago
Alireza ▴ 20
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?
Searching always an option. https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format
This link is about the GVCF format. my question is about the GVF format. I think these two formats are different.
Here is information about the GVF variant format: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-8-r88
You may want to email Ensembl help desk and ask. Provide examples to them. GVF seems to be only used by 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.
Thanks for your response.
Also, I wrote an easy script to convert GVF to VCF.
I think it works well.