question about Mutation Annotation Format (MAF) variant classifications
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11 weeks ago

I am working with some Mutation Annotation Format (MAF) files downloaded from ICGC (well, not directly downloaded, but downloaded as “simple somatic mutation format" files and converted to MAF format with the icgcSimpleMutationToMAF function of the R Maftools package), and I wanted some clarity on how the "Variant_Classification" categories are defined. Most are semi-self-explanatory, but I was wondering about how 5' flank and 3' flank calls are made as opposed to IGR (intergenic region). Is it just defined as some fixed distance from the start and end of the transcribed region? Thanks!

annotation ICGC MAF R • 261 views
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Is it just defined as some fixed distance from the start and end of the transcribed region?

Most probably, yes. You may have to dig through MAF documentation to find the exact cutoff point.

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Thanks - yes, I've been trying to find it in the online documentation, but without any success so far.

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