Mutation data with Variant Allele Frequency at CbioPortal

Question

[ruhollah]

I am searching for publicly available maf-like files that contain variant allele frequency (VAF) data for human prostate tumors, as I need to compare it with our in-house mice prostate tumor data.

The CBioPortal github has data_mutations.txt and data_mutations_extended.txt files, however, none of them includes VAF information.

Can you assist me in finding a database that offers this type of data?

[barslmn]

VAF may also refer to variant allele fraction. But if you want frequencies you can annotate these files with frequencies from alfa or gnomad using an annotation tools like VEP.

Answer 1

[ruhollah]

Ok! I just figured it out. So, here I share the solution for future reference in case others have a similar question:

To calculate variant allele frequencies (VAF) using a cBioPortal mutation_data file, the necessary information can be found in the t_alt_count and t_ref_count columns (as per cbioportal authors are not required to provide these columns, thus some publications might miss these columns, in which case this method is not applicable). To obtain the variant allele frequency (VAF):

VAF =  t_alt_count / (t_alt_count + t_ref_count)