MAF vs VAF
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4.4 years ago

Hi all.. Anyone can help explaining the difference between MAF (mutant allele) and VAF (variant allele) frequency? Thanks

sequencing • 8.8k views
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Could be Multiple Ambiguous Formats ...

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As far as I know the 'M' in MAF means minor and not mutant. I think VAF and MAF are the same.

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Note that even "minor allele frequency" is overloaded here. In a traditional sense, minor allele frequency refers to the frequency of an allele in a population of patients from a germline sampling. The variant allele frequency is typically used in a cancer setting to describe the proportion of reads with the variant allele within a single patient. The best option is to define what you mean very specifically; use in the literature is not a good guide, as is evidenced by the comments here.

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Yes, and I would favour the term Variant Allele Fraction (or Variant Allelic Fraction) rather than Variant Allele Frequency for this reason too!

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Looks like the MAF acronym is being repeatedly hijacked!

There is:

  • MAF, minor allele frequeny
  • MAF, mutation annotation format
  • MAF, mutant allele fraction

Edit: As per Wouter's ultimate conclusion, you can consider mutant allele fraction and VAF as the same. Minor allele frequency is more used in GWAS studies.

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Don't forget the Multiple Alignment Format.

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