Question: Conversion of Vep.vcf to MAF format?
0
gravatar for thind.amarinder
7 weeks ago by
Italy
thind.amarinder20 wrote:

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 snp vep genome maf • 134 views
ADD COMMENTlink modified 6 weeks ago • written 7 weeks ago by thind.amarinder20
1
gravatar for abedkurdi10
6 weeks ago by
abedkurdi1030
abedkurdi1030 wrote:

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

ADD COMMENTlink written 6 weeks ago by abedkurdi1030

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

ADD REPLYlink written 6 weeks ago by thind.amarinder20

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by abedkurdi1030
0
gravatar for thind.amarinder
6 weeks ago by
Italy
thind.amarinder20 wrote:

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

ADD COMMENTlink written 6 weeks ago by thind.amarinder20

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

ADD REPLYlink written 6 weeks ago by abedkurdi1030

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 REPLYlink written 6 weeks ago by thind.amarinder20
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