VCF file (annotated with snpeff) to MAF

Question

[JJ]

Hi all,

I've read the posts here on VCF to MAF conversion (e.g. Converting Vcf File To Maf ). However, I could not manage to convert a snpeff annotated VCF file to MAF. Is there any way? Any tool that can do this? or do I need to use VEP for annotation?

Thanks! JJ

[Ram]

I could not manage to convert

Please be more specific - what happened when you tried? Did you see any error message? What was the message? If there was no message, how did you know you did not succeed?

[JJ]

I am sorry for not being more specific - it's a known issue: https://github.com/mskcc/vcf2maf/issues/174 the converter does not work with snpeff annotated files - hence I was wondering if there is a tool that could do that.

Answer 1

[tsy19900929]

https://github.com/tsy19900929/snpeffToMaf