How to run variant effect analysis in Ensembl?

Access the Ensembl Variant Effect Predictor (VEP)

• Visit the Ensembl website and navigate to the Variant Effect Predictor (VEP) page.

 

• Ensure you have access to an Ensembl account if required, though basic VEP functionality is generally accessible without an account.

Prepare Variant Data

• Collect and format your variant data, typically in VCF (Variant Call Format) or as a simple list containing genomic coordinates of the variants.

 

• Ensure variants are listed as chromosome, position, reference allele, and alternate allele, properly formatted according to VEP specifications.

Input Variants into VEP

• On the VEP page, choose the option to input your variants either by file upload or by pasting data directly into the provided text area.

 

• Select the appropriate genome assembly version (e.g., GRCh38 or GRCh37) that matches your data.

Configure VEP Options

• Adjust analysis settings based on your research needs. Options include choosing specific transcript databases, filtering by consequence types, or adjusting upstream and downstream sequence lengths.

 

• Select additional output fields if required, such as gene information, protein domains, or regulatory feature impacts.

Run the Analysis

• Submit your job for processing by clicking the "Run" button. Note that this process may take some time depending on the number of variants and the selected options.

 

• Wait for analysis to complete. You will be redirected or informed via email (if configured) when results are ready.

Review Output Results

• Access the results page to view a comprehensive table summarizing the effect of each variant on gene function, possible phenotypic consequences, and any other selected annotations.

 

• Download results in preferred formats such as tab-delimited or VCF files for local analysis or to share with collaborators.

Interpret Findings

• Analyze the effect predictions and annotations to evaluate the potential biological significance or pathogenicity of the variants in your dataset.

 

• Correlate findings with additional literature or databases for further insights or validation of variant impacts in specific contexts.