[ensembl-dev] Mouse Gene Symbols on VEP73

[Will McLaren]

Hi Duarte,

Are you sure you have everything (cache, API, script) up to date?

It works fine for me using --symbol

Try the following input:

11      3762252 3762252 C/T     1

This is my output:

> perl variant_effect_predictor.pl -offline -i mouse_test.txt -force
-symbol -species mus_musculus -dir /data/blastdb/Ensembl/vep/ -o stdout
## ENSEMBL VARIANT EFFECT PREDICTOR v73
## Output produced at 2013-11-06 11:12:41
## Connected to
## Using cache in /data/blastdb/Ensembl/vep//mus_musculus/73
## Using API version 73, DB version ?
## Extra column keys:
## DISTANCE : Shortest distance from variant to transcript
## SYMBOL : Gene symbol (e.g. HGNC)
#Uploaded_variation     Location        Allele  Gene    Feature
Feature_type    Consequence     cDNA_position   CDS_position
 Protein_position        Amino_acids     Codons  Existing_variation
 Extra
rs26884575      11:3762252      T       ENSMUSG00000020435
 ENSMUST00000135250      Transcript
 intron_variant,nc_transcript_variant    -       -       -       -       -
      -       SYMBOL=Osbp2
rs26884575      11:3762252      T       ENSMUSG00000020435
 ENSMUST00000070552      Transcript      intron_variant
  -       -       -       -       -       -       SYMBOL=Osbp2
rs26884575      11:3762252      T       ENSMUSG00000020435
 ENSMUST00000127371      Transcript      intron_variant
  -       -       -       -       -       -       SYMBOL=Osbp2
rs26884575      11:3762252      T       ENSMUSG00000020435
 ENSMUST00000155197      Transcript      intron_variant
  -       -       -       -       -       -       SYMBOL=Osbp2

Cheers

Will



On 6 November 2013 11:00, Duarte Molha <Duarte.Molha at ogt.com> wrote:

> Dear Developers
>
>
>
> I am running an annotation of a mouse sample and would like to output the
> gene name in addition to the ensembl gene identifier…
>
> Is there a way to do this on the script? I used the symbol field but that
> in not outputting anything
>
>
>
> (I’m on v73)
>
>
>
> Thanks
>
>
>
> Duarte Molha
>
>
>
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