Conversion of Vep.vcf to MAF format?
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2.4 years 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 • 2.1k views
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2.4 years ago
abedkurdi10 ▴ 190

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

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

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

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2.4 years ago

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

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

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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
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