Are There Any Tools To Convert Gatk Vcf Format To A Maf File ?
1
3
Entering edit mode
7.7 years ago

I am doing a project about leucocythemia,I called SNP and InDel with GATK and got some vcf files.Now I want to use genome MuSiC , but I cannot convert the vcf file to a MAF file ,though I annotated after Snpeff. I could not convert with the code http://code.google.com/p/ngs-analysis/source/browse/modules/somatic/vcf2maf.py Do you have any advice?

music gatk maf vcf • 4.9k views
ADD COMMENT
2
Entering edit mode

Please define what you mean by that script not working. Did you receive an error? Was the output gibberish? Was the output simply wrong?

ADD REPLY
0
Entering edit mode

vcf2maf.py converts a VCF to TCGA Mutation Annotation File (MAF). The galaxy tool vcf_to_maf_customtrack1 (URL above) converts a VCF file into a Multiple Alignment Format (MAF) file suitable for display at genome browsers.

ADD REPLY
1
Entering edit mode
7.5 years ago

I recently posted a VCF->MAF conversion script at: github.com/ckandoth/vcf2maf. 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 COMMENT

Login before adding your answer.

Traffic: 2760 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6