AnnoVar with custom genomes?
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2.1 years ago

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?

AnnoVar Annovar • 398 views
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