Mutations to use in mutational signature analysis

Question

[jc]

When performing mutational signature analysis with R packages such as deconstructSigs and SomaticSignatures, should all SNVs be used or just nonsilent SNVs?

Answer 1

[Kevin Blighe]

I believe the choice is yours. It would make intuitive sense to include missense mutations, though, and not intronic or intergenic variants. Basically, you use whatever you want to use.

Kevin