Question: VEP cache trancript versions
0
gravatar for Chadi Saad
7 days ago by
Chadi Saad70
France
Chadi Saad70 wrote:

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

ADD COMMENTlink modified 4 days ago by Michal @Ensembl20 • written 7 days ago by Chadi Saad70
0
gravatar for JC
7 days ago by
JC10k
Mexico
JC10k wrote:

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

ADD COMMENTlink written 7 days ago by JC10k

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

ADD REPLYlink written 7 days ago by Chadi Saad70
0
gravatar for Michal @Ensembl
4 days ago by
UK, Cambridge, EMBL-EBI
Michal @Ensembl20 wrote:

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

ADD COMMENTlink written 4 days ago by Michal @Ensembl20
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