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

[Avril Coghlan]

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