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

[Avril Coghlan]

Dear Emily,

That's great, thanks very much for the link, I'll try to follow these instructions.

Regards and thanks,
Avril

On 16 Jan 2014, at 13:35, Emily Pritchard <emily at ebi.ac.uk> wrote:

> 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
> 
> 
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