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?
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.