Vcf2Maf currently doens't work with VEP annotation

[FriederikeHanssen]

Description of the bug

It is currently not possible to annotate VCF files with vcf2maf. This issue is raised already in the vcf2maf repo (mskcc/vcf2maf#335) . In the meantime, it is recommended to annotated the VCF files with VEP in nf-core/sarek and then supply them as input here.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[famosab]

I will try to include the annotation subworkflow from nf-core which is also used in sarek. Then we do not have to wait for vcf2maf to fix it and can avoid using two pipelines.