When a maf file indicates the nucleotide identity at a mutant locus, is this always done with respect to the coding strand, even when the mutation occurs in a negative-sense reading frame? In other words, if we have 5' ACGTA 3', and the gene is negative sense (5' TACGT 3'), does a mutation at position 4 to C indicate that we have 5' TACCT 3' (negative sense), or 5' ACGCA 3' in the positive sense strand?
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I assume you're talking about TCGA's Mutation Annotation Format files. Column 8 shows the strand, and they describe that "only the positive strand is an accepted value". In general, it's a standard practice to report variants on the positive strand regardless of which direction transcription happens.
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Cyriac Kandoth
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