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!