Question: Converting Vcf File To Maf
gravatar for l.pirhaji
7.4 years ago by
l.pirhaji80 wrote:

I'm going to use VarScan2 and MuSiC software to identify mutated genes from exome sequencing data.

at first, I used VarScan2 to identity somatic mutations. I will then use MuSiC to identify significantly mutated genes from VarScan2 results. However, the output file generated from VarScan2 is in VCF format, but MuSiC only accepts MAF file format as an input.

I was wondering if there is any available tools for converting VCF file format to MAF.

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ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 7.4 years ago by l.pirhaji80

Possible duplicate of VCF to MAF (Mutation Annotation Format) Conversion ?

ADD REPLYlink written 7.4 years ago by Eric Normandeau10k
gravatar for Cyriac Kandoth
7.0 years ago by
Cyriac Kandoth5.5k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.5k wrote:

I recently posted a VCF->MAF conversion script at: It's plenty documented so that you understand what information is lost in translation.

Briefly - each VCF variant must be annotated to only one of all possible gene transcripts/isoforms that it might affect. This selection of a single affected transcript/isoform per variant, is often subjective. For now, the scripts tries to follow best-practices: it chooses the "worst" effect on the "best" transcript. If there are multiple such candidates, it annotates the variant effect on the longest "best" transcript.

ADD COMMENTlink modified 2.8 years ago • written 7.0 years ago by Cyriac Kandoth5.5k

Thanks for the script but the current version still requires snpEff yet I have already annotated using snpEff. Could you please push a version that doesn't depend on snpEff? Thanks again!

ADD REPLYlink written 6.7 years ago by tayebwajb90

The script skips snpEff annotation for an input VCF named file.vcf if it finds an annotated VCF named file.anno.vcf. You can use this as a workaround. Otherwise, try this fork of the script:

Update: I released vcf2maf v1.1 that allows you to use a VCF that is already annotated with snpEff or Ensembl's VEP.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Cyriac Kandoth5.5k
gravatar for mdm-two
7.4 years ago by
mdm-two230 wrote:

Will read in an annotated vcf file outputted by SNPEff It will parse and output the data in tcga maf format (currently v 2.3

By default, every effect and transcript annotated per variant will be outputted as a row in the maf file. (In other words you will need to filter to one row per sample per variant)

This included somatic caller support for varscan and GATK.

There are many other vcf2maf alternatives such as

You might also want to research Ensembl VEP for VCF annotation:

ADD COMMENTlink written 7.4 years ago by mdm-two230
gravatar for mdm-two
7.2 years ago by
mdm-two230 wrote:

Same question answered here: converting VCF file to MAF

ADD COMMENTlink written 7.2 years ago by mdm-two230
gravatar for rse
4.6 years ago by
rse90 wrote:

Hi Cyriac, i used vcf2maf perl script. Installed vcf2maf-master, vep. But getting an error - WARNING: Chromosome 1 not found in cache on line . What can be the reason?

ADD COMMENTlink written 4.6 years ago by rse90

Please don't write a question in a section that's meant for an answer. Either start a new question, or submit an issue at

ADD REPLYlink written 4.6 years ago by Cyriac Kandoth5.5k
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