Use VEP (ensembl) with specific database e.g. dbSNP 144

Question

[romain.lannes]

Hi,

I am working with medical data, in collaboration with a diagnostic platform. I am used to working with VEP. IMO it is an awesome tool that simplifies analyses.

But I must use the same database they use in the diagnostic platform. Unfortunately, they do not update their database regularly, mainly for reproducibility.

My problem is that when downloading VEP cache it is already built on the latest databases (which is handy 99% of the times). Does it exist a way to build a custom VEP cache providing the specific database version I want to use? mainly use specifics version of dbSNP, COSMIC and CLINVAR.

Any help would be really appreciated.

Answer 1

[Ben Moore]

Hi romain.lannes,

You can install archive versions of the VEP tool that correspond to database versions that you are interested in: http://dec2015.archive.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html

For example, you can see from the documentation that Ensembl 83 was the last Ensembl version to use dbSNP 144 as a variation data source: http://dec2015.archive.ensembl.org/info/genome/variation/sources_documentation.html

We strongly recommend that you download/use the VEP Cache version which corresponds to your Ensembl VEP installation. This is mainly due to the fact that the VEP Cache (data content and structure) is generated every Ensembl release, regarding the data and API updates for this release, therefore the cache data format might differ between versions (and be incompatible with a newer version of the Ensembl VEP tool).

Best wishes

Ben