Normally, I would use the vcf2maf scripts to convert a VCF to a MAF (or vice versa).
This is great software, but on my system, perl scripts with dependencies are easy to break. (Here it uses VEP.)
Are there any other alternatives to this?
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Sign up to join this communityNormally, I would use the vcf2maf scripts to convert a VCF to a MAF (or vice versa).
This is great software, but on my system, perl scripts with dependencies are easy to break. (Here it uses VEP.)
Are there any other alternatives to this?
You can use annovar to annotate the vcf, then convert it to maf using the function annovarToMaf
of maftools bioconductor package.