[ensembl-dev] Is it possible to reuse VEP (75_37) output for Ensembl core data 82_37

[Sarah Hunt]

Hi Treesa,

We switched to using GRCh38 in release 76, so release 75 was the last 
time GRCh37 gene annotation was updated. We are maintaining a GRCh37 
site and database and these have been updated with variant and 
regulatory data which you would have access to in a new VEP run, but 
there is no change to the transcripts.

If you are only interested in consequences for public variants, you 
could look at the file:

ftp://ftp.ensembl.org/pub/grch37/update/variation/vcf/homo_sapiens/Homo_sapiens_incl_consequences.vcf.gz

You don't say how you ran VEP previously but there is information you 
may find useful on how to make it run faster here:

http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html

Best wishes,

Sarah

On 03/12/2015 06:15, binit treesa wrote:
> Hi Ensembl Team,
>
> Currently we are using  homo_sapiens_core_82_37 database. Previously 
> we created VEP output for homo_sapiens_core_75_37 version. It took lot 
> of time for us to run VEP with all varaints.
>
> We think that homo_sapiens_core_82_37 core database contains more 
> records and there will be count difference (increase) in number of 
> genes and transcripts. Some genes in version 75 will be retired and 82 
> version do not have that well.
>
> Can we use VEP output generated for homo_sapiens_core_75_37 database,  
> for homo_sapiens_core_82_37 data if the Ensembl gene id, transcript id 
> ,co-ordinates and alleles are matching in VEP output file?
>
> Also Whether it is  possible to get VEP information from any sources 
> for Ensembl core  82_37 without running VEP perl script?
>
> Thanks in advance,
> Treesa Binit
>
>
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