Converting Vcf File To Maf

Question

[l.pirhaji]

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.

[Eric Normandeau]

Possible duplicate of Vcf To Maf (Mutation Annotation Format) Conversion ?

[rse]

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?

[Cyriac Kandoth]

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 https://github.com/mskcc/vcf2maf/issues

Answer 1

[Cyriac Kandoth]

I recently posted a VCF->MAF conversion script here. 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.

[tayebwajb]

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!

[Cyriac Kandoth]

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.

Answer 2

[mdm-two]

http://code.google.com/p/ngs-analysis/source/browse/modules/somatic/vcf2maf.py

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 http://goo.gl/2Shtq )

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

https://github.com/Sage-Bionetworks/vcf2maf/blob/master/vcf2maf/vcf2maf.py

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

Answer 3

[mdm-two]

Same question answered here:

• http://seqanswers.com/forums/showthread.php?t=16740
• Converting Vcf File To Maf