absence of gene symbol when selecting "most severe consequence" in VEP

Question

[nazaninhoseinkhan]

Dear all,

I am using Variant Effect Predictor (VEP) to annotate copy number alteration in cancer.

In the output there are several consequences per gene, so I decided to filter the results to have the most severe consequences per gene.

However in the results table the symbol and gene name columns are completely empty and only the consequences have been reported.

Can you tell me what is the best filtering option for the purpose of shrinking the output?

Thank you in advance

Nazanin

Answer 1

[Emily]

Which exact option did you select? Some options (eg "Show most severe consequence per variant") will not give you a gene, since that selected consequence may occur on more than one gene, whereas others (eg "Show one selected consequence per gene") will give you a line for each gene hit. This document describes what all the different options will give you.

[nazaninhoseinkhan]

Hi Emily,

I had used "show the most severe consequence per variants".

Thanks for your comment.

I will try other options