[ensembl-dev] VEP Cache Gene List

[Michael Milton]

Yes we are using GRCh37. So we looked at the Ensembl release 75 genes (just using biomart) and there are still a number of gene symbols that VEP is outputting that don't occur in the GRCh37 Ensembl database at all (as far as I can tell anyway).


Namely:

  *   ARMCX5-GPRASP2
  *   C7orf10
  *   PCDHGB5
  *   PHOSPHO2-KLHL23
  *   THEG5
  *   UQCRHL
  *   ZSCAN26

There are others (100-200 I believe?) but this is just a small sample.

Any ideas where these symbols are derived from?

________________________________
From: dev-bounces at ensembl.org <dev-bounces at ensembl.org> on behalf of Will McLaren <wm2 at ebi.ac.uk>
Sent: Wednesday, 3 August 2016 10:46:02 PM
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP Cache Gene List

Hi Michael,

I assume from this that you are using the GRCh37 assembly? Ensembl and therefore VEP annotations on GRCh37 were frozen at Ensembl release 75 as we have moved our main annotation pipelines to GRCh38.

See the about box on the RH side of http://grch37.ensembl.org/index.html

Regards

Will McLaren
Ensembl Variation

On 3 August 2016 at 06:41, Michael Milton <michael.milton at unimelb.edu.au<mailto:michael.milton at unimelb.edu.au>> wrote:

Hi, I'm using VEP with a downloaded cache, and it seems that VEP is annotating some non-hgnc gene symbols or at least outdated symbols. I need a gene list including all possible genes that VEP could output for a downstream application. Is there a definitive list of genes that VEP could output? Otherwise, what source is used to build the VEP cache?


Some of the superceded gene symbols it's outputting, using the Ensembl 83 refseq cache, are:

  *   GLTPD1
  *   C1orf86
  *   C7orf63
  *   PCNXL3

Thanks!


_______________________________________________
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/20160804/76d0e995/attachment.html>