Snippy without reference (suggestion)

[cmkobel]

I've been looking for a SNP-caller that does not depend on a reference genome.

How hard would it be make snippy work on the core genome of a set of microbial isolates? We can probably assume that the most common variants are ancestral.

This might be useful, if a reference is not representative of a isolate set.

Do you think it would make any sense?

Cheers, Carl.