I am trying to get information from somatic nucleotide variant of patients.
I hope to make mutation signature like cosmic. (Below is link)
According to the site, all mutation signature are referred to by the pyrimidine of the mutated Watson–Crick base pair.
So there are only 6 types of nucleotide substitution.
C>A, C>G, C>T, T>A, T>C, and T>G
I am wondering how to count other nucleotide substitutions.
For instance, is G>A substitution considered as C>T substitution and added to C>T substitution?
Or is the change not counted (i.e 0) ?
My colleague said that in the case, they are not counted. However, I think that the comment is wrong.
This is because there will be too much loss of information about substitution.
I believe that G>A substitution is considered C>T.
Please give me your opinion.