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.
•
written
by
l.pirhaji •
3 answers
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.
•
written
by
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.
•
written
by
Cyriac Kandoth
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.
Same question answered here:
Log in to answer this question.
-
maftools do not find differentially mutated genes while bcftools isec have a lot of locus for each …
written by omicsresearch •
-
Exome-seq; Which tools to predict significantly muated genes .
written by Chirag Nepal
-
Where to get somatic mutations from WGS data?!
written by dankoc •
-
converting VCF to MAF fro mouse data
written by ksymeonidh •
-
Are there recommended steps if MuSiC reports too many significantly mutated genes
written by Collin
-
PathScan: How to control for gene-specific differences in background mutation rates?
written by Christian
-
Significantly mutated genes without control
written by aikaterini.symeonidi •
-
Genome MuSic: Mutation frequency for single gene of interest across all available cancer types (pan…
written by atn3 •
-
Music Analysis Workflow
written by Pascal
-
Genome Music Bmr Calc-Bmr Returning All Zeros Under "Mutations" And "Bmr" In Gene_Mrs File
written by sndorman •
Possible duplicate of Vcf To Maf (Mutation Annotation Format) Conversion ?
Hi Cyriac, I used vcf2maf perl script. Installed vcf2maf-master, vep. But getting an error -
What can be the reason?
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