Conversion of Vep.vcf to MAF format?

Question

[Thind amarinder]

I have Vep.vcf files and I would like to convert it into MAF. But I do not want to execute VEP again, as required by vcf2maf. What are the other possibilities?

Answer 1

[abedkurdi10]

While it is no more maintained, but try this: https://github.com/cbare/vcf2maf

[Thind amarinder]

not really, I have annotated vcf by VEP. not .vcf

[abedkurdi10]

Maybe you can use bcftools +split-vep and extract the variants in tabulated format with specific order of the fields.

Answer 2

[Thind amarinder]

I got my answer. It is possible with https://github.com/mskcc/vcf2maf/releases/tag/v1.1.0

[abedkurdi10]

but this is the same vcf2maf.pl which requires vep to run

[Thind amarinder]

I am trying, they wrote If you already annotated a VCF with either VEP or snpEff, you can use those directly:

perl vcf2maf.pl --input-vep test.vep.vcf --output-maf test.maf
perl vcf2maf.pl --input-snpeff test.snpeff.vcf --output-maf test.maf