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VCF file (annotated with snpeff) to MAF

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

genome sequencing
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updated by tsy19900929 • tsy19900929 • written by JJ JJ

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?

• 1 views • link
written by Ram Ram

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.

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written by JJ JJ

1 answer

https://github.com/tsy19900929/snpeffToMaf

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written by tsy19900929 • tsy19900929

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