Homomorphic encryption, presumably? It's not impossible. But I also think it's overkill. Also, I don't know of good open source software that lets me do the kind of analysis I want even on non-encrypted data.
That would not be very comforting, this would mean that even encrypted, we can know stuff from the encrypted form, which kinds of defeat the purpose unless I'm missing something.
How are scientists able to work on encrypted genomes?