VEP cache trancript versions

Question

[Chadi Saad]

I have a same variant obtained once on GRCH37 and once on GRCH38 I want to annotate it with VEP to obtain the HGVS annotation. So I use VEP (v100) to annotate both variants.

On GrcH37, the variant is annotated with NM_001160184.1, while for GRCH38, this variant is annotated with NM_001160184.2.

It seems that the problem is due to the fact that VEP don't use the same RefSeq database (see : https://m.ensembl.org/info/docs/tools/vep/script/vep_cache.html)

RefSeq version:

2019-06-28 (GCF_000001405.39_GRCh38.p13_genomic.gff) for GRCh38 data 2019-11-01 (GCF_000001405.25_GRCh37.p13_genomic.gff) for GRCh37 data

Why VEP does not use use the same GFF file ? how to obtain the annotation with the same transcript on both genome versions ? (NM_001160184.1 for grch 37 and 38)

Thanks

Answer 1

[Michal @Ensembl]

Hi Chadi, I'm afraid there's no "same" GFF file for GRCh37 and GRCh38. You can find all RefSeq versions under the following link: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/ We import the latest RefSeq version for both builds. Hope that helps. Best wishes, Michal Ensembl Helpdesk

Answer 2

[JC]

Why VEP does not use use the same GFF file ?

They can't, both reference genomes are not the same, so the annotation and coordinates in some regions are different

[Chadi Saad]

we can't have something like GCF_000001405.39_GRCh37_genomic.gff (the same GCF used for GRCH38 GCF_000001405.39_GRCh38.p13_genomic.gff) ? why using GCF_000001405.25 for GRCh37