Dear all, I heard many times about possibility to convert annotated vcf to maf with vcf2maf by rewriting of name to *.vep.vcf (which marks that vcf is already annotated). But even when I do it, the vcf2maf program wants to annotate it again, which I don't want. Can you please advice me how to make it work without annotation?
$ vcf2maf.pl --input-vcf input.vep.vcf --output-maf output.vep.maf --vcf-tumor-id input_TUMOR --vcf-normal-id input_NORMAL --tumor-id input_TUMOR normal-id input_NORMAL --buffer-size 100 --ref-fasta
/exports/eddie/scratch/s1959373/external/human_g1k_v37.fasta --filter-vcf 0
STATUS: Running VEP and writing to: ./input.vep.vep.vcf ERROR: Cannot find VEP script in path: /home/..
Thank you very much!