VCF to MAF using oncotator

Question

[hamrejr]

Does anyone know the bash code to convert a vcf to a maf in oncotator? Thanks!

[Dave Carlson]

Do you have to use Oncotator? It's no longer updated or supported by the BROAD. It might be useful to try Funcotator instead (part of GATK). There is a very detailed tutorial here:

https://gatk.broadinstitute.org/hc/en-us/articles/360035889931-Funcotator-Information-and-Tutorial