Question: VCF file (annotated with snpeff) to MAF
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gravatar for JJ
12 months ago by
JJ490
JJ490 wrote:

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

sequencing genome • 475 views
ADD COMMENTlink modified 12 months ago by RamRS25k • written 12 months ago by JJ490

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?

ADD REPLYlink written 12 months ago by RamRS25k

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.

ADD REPLYlink written 12 months ago by JJ490
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