Hello!

I am doing some variant calling on mice against mm10, but with some human genes added to the reference genome during mapping, because the mice are gene-edited. Obviously AnnoVar doesn't know what to do with these reads but I would still like to have somewhat informative output like syn or non-syn, etc.

Is there a standardized way to deal with these custom circumstances, or must I do some ugly hack on existing mm10 AnnoVar files?