[ensembl-dev] Mouse Gene Symbols on VEP73

[Duarte Molha]

Hi Will

I just realised the issue. I had rearranged the field order and the fields option in VEP seems to be case sensitive.. I has calling in small caps and it does not display. When changed to SYMBOL it works flawlessly.

Cheers,

Duarte

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 06 November 2013 11:14
To: Ensembl developers list
Subject: Re: [ensembl-dev] Mouse Gene Symbols on VEP73

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<http://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<mailto: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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