Variant annotation and effect prediction
All data and files for this section can be found in the EBI training FTP.
Annotation and Variation with Ensembl
Trainers: Jose Maria Gonzalez Perez-Silva and Jamie Allen
Overview: In this session, we will learn the steps, data sources, and software used in Ensembl’s genome annotation. As well as learning the basics of the process.
Learning outcomes:
By the end of this session, you will be able to:
- Describe Ensembl and its resources for gene annotation
- Describe Ensembl VEP to identify variants of interest
Materials:
- ‘Annotation and Variation with Ensembl’ slides
- ‘Variant Annotation with Variant Effect Predictor’ slides
Ensembl ‘Variant Effect Predictor’ tutorial
Trainers: Jamie Allen and Syed Nakib Hossain
Overview: This session provides an overview of the Ensembl ‘Variant Effect Predictor’ (VEP) tool, used to determine the effect of your variants on genes, transcripts, and protein sequence, as well as regulatory regions.
Learning outcomes:
By the end of this session, you will be able to:
- Use the Ensembl Variant Effect Predictor (VEP) to annotate variants
- Describe common input formats for VEP
- Practice different command line options for VEP
Materials: