Ensembl – Variant Effect Predictor

Trainer: Aleena Mushtaq

Overview: During the three sections of this course, a single example was used throughout, using different EMBL-EBI tools resources at each stage of the analysis pipeline. In this section, a VCF file was run through the Ensembl Variant Effect Predictor (VEP).

Learning outcomes:

After this section you should be able to:

• Describe the main functionality and options available for the Ensembl Variant Effect Predictor (VEP)
• Annotate a variation dataset using the web-based VEP tool
• Interpret the output of the VEP and navigate to other EMBL-EBI resources to further assess variant effects on proteins

Materials:

• Interpreting the effects of genetic variants on protein structure and function – Ensembl slides
• VEP demo
• Variants demo VCF
• Practical VCF
• Practical output VCF