Question: Are There Any Tools To Convert Gatk Vcf Format To A Maf File ?
gravatar for lixuenan200806
6.8 years ago by
lixuenan20080630 wrote:

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 Do you have any advice?

maf gatk vcf music • 4.5k views
ADD COMMENTlink modified 6.6 years ago by Cyriac Kandoth5.5k • written 6.8 years ago by lixuenan20080630

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 REPLYlink modified 6.8 years ago • written 6.8 years ago by Devon Ryan95k

ADD REPLYlink written 6.8 years ago by stolarek.ir650 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 REPLYlink written 6.8 years ago by mdm-two230
gravatar for Cyriac Kandoth
6.6 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 written 6.6 years ago by Cyriac Kandoth5.5k
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