I am using SomaticSignatures package. When we extract sequence context of single nucleotide variants using the command like this
sca_motifs = mutationContext(sca_vr, BSgenome.Hsapiens.1000genomes.hs37d5)
we get two additional columns in vranges, alteration and context.
If ref is G and alt is A, then CT is mentioned in alteration column, which is according to the opposite strand. I want to ask whether in this case neighboring nucleotides provided in context column is also according to the opposite strand.
Would someone please answer my question?