Conversion of Vep.vcf to MAF format?
2
0
Entering edit mode
13 months ago

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?

cancer vep maf snp genome • 727 views
ADD COMMENT
1
Entering edit mode
13 months ago
abedkurdi10 ▴ 30

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
13 months ago

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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
ADD REPLY

Login before adding your answer.

Traffic: 2086 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6