question about Mutation Annotation Format (MAF) variant classifications

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3.3 years ago

Charles Murtaugh ▴ 50

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 • 1.2k views

ADD COMMENT • link 3.3 years ago by Charles Murtaugh ▴ 50

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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.

ADD REPLY • link 3.3 years ago by Ram 44k

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

ADD REPLY • link 3.3 years ago by Charles Murtaugh ▴ 50

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