How to keep quality annotations in MAF file using vcf2maf?

Question

[Gonzalo]

Hi everyone, I have a query regarding the use of vcf2maf.

I used Ensembl vep to annotate a vcf file, then I used vcf2maf to convert the file to .MAF format, then I used maftools.

The problem I have is when using vcf2maf I lose several important annotations such as Count, Coverage, Frequency, QUAL. The script works fine, but the columns t_depth, t_ref_count, and t_alt_count are left empty.

These annotations are not lost in the vep output file.

Does anyone know if it is possible to keep these annotations in the MAF file?

Thanks in advance for any help!