[ensembl-dev] VEP 76 build 37

[Eva Goncalves Serra]

Thanks a lot Will, this was very useful.

Best wishes,

Eva

From: Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Tuesday, 23 September 2014 09:21
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] VEP 76 build 37

Hi Eva,

That should be enough to ensure the correct assembly. There is a --assembly flag that you can use to be sure.

If you only have one cache installed for the software version (76) then it will be automatically used without the need for --assembly - check the headers in your output and you should see the cache directory. If you have two versions (i.e. both GRCh37 and GRCh38) then in --offline mode the VEP will prompt you to select one using --assembly.

If you use --cache instead of --offline (which you might do in order to use rsIDs as input, for example), then you might also need to add "--port 3337" since on the default port VEP will use GRCh38. However, the VEP will warn you if the assembly version of the database it connects to and the cache are different.

See http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly for more details of all of this.

Regards

Will McLaren
Ensembl Variation

On 22 September 2014 17:19, Eva Goncalves Serra <egs at sanger.ac.uk<mailto:egs at sanger.ac.uk>> wrote:
Hi,

I have installed vEP 76 and downloaded the homo_sapiens_vep_76_37 cache files and the fasta Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.
I want to make sure I am using the GRCh37 when using VEP. Do I need to specify anything in particular other than the cache dir?

Thanks,

Eva

_______________________________________________
Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140923/6fff8d92/attachment.html>