Double base substitutions annotation

[andreyurch]

Dear Inigo,

I found the following message while running the tools: "Mutations observed in contiguous sites within a sample. Please annotate or remove dinucleotide or complex substitutions for best results." I do have many double-base substitutions (due to skin cancer samples). I can annotate them, but how should I provide the file to the tool afterwards.

Best regards,
Andrey