vcf2maf cosmic annotation

Question

[anubratadas]

when I convert vcf files to maf files using default parameters in vcf2maf, i do not get COSV/COSM id annotations. what is the vcf2maf equivalent of vep --everything?

[Cyriac Kandoth]

vcf2maf uses vep under the hood but at some point, I replaced "vep --everything" with each of the arguments that correspond to "vep --everything". I think the specific argument that populates COSV/COSM IDs is "--var_synonyms" which seems new and is not yet incorporated into vcf2maf. For now, you can add "--var_synonyms" to this VEP command in your local copy of vcf2maf.

[anubratadas]

Thank you so much Cyriac Kandoth for clearing my doubt!