Hello

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?

If the alteration is transformed to a pyrimidine reference (T or C), the mutation context is also transformed accordingly by default. You can check this by disabling the transformation in the mutationContext function, by setting unify = FALSE.