[ensembl-dev] predicting consequences for SNPs, for a custom Ensembl database

[Emily Pritchard]

Hi Avril

Yes. You'll need to create a GTF file of your gene annotation, which you 
can then use to make a VEP cache:
http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gtf

You can then use the cache to run the VEP against (more info on the page 
above).

Hope this helps

Emily
Ensembl helpdesk

On 16/01/2014 13:23, Avril Coghlan wrote:
> Dear Ensembl Dev,
>
> My colleague (Eleanor Stanley) has built a Strongyloides ratti 'core' Ensembl database for one of the species studied in our group (Strongyloides ratti).
> We also have a VCF file of SNPs that we have found in S. ratti based on our data from our group.
>
> I'm wondering is it possible for me to predict consequences of the SNPs, using Ensembl's Variant Effect Predictor Tool? If so, are there any examples/documentation available on how I can do this?
> I would be very grateful for any help.
>
> Kind Regards,
> Avril
>
> Avril Coghlan
> Parasite Genomics Team
> Sanger Institute
>
>
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-- 
Dr Emily Pritchard
Ensembl Outreach Officer

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK