vcf2maf VEP annotated VCF conversion

Question

[Martina]

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!

Martina

[Thind amarinder]

@martina I was wondering if you have solved the problem. I have vep.vcf file and want to convert it into MAF.

[Martina]

Hello, yes, the answer is just in the comment below: Hello, this issue said you need to COPY your vcf and name "*.vep.vcf", not mv command.

So you need to have both .vcf and .vep.vcf files in the folder.

Have a nice day, Martina

Answer 1

[MatthewP]

Hello, this issue said you need to COPY your vcf and name "*.vep.vcf", not mv command.

Answer 2

[Martina]

Oh.. Thank you very much :)