how to get common variants between two species?

Question

[kk.mahsa]

i have sequencing data for two species, that they are able to mate together. now i want to extract common variants between them. To do this, must i map two data set in one reference genome or there are other ways?

thanks in advance

Answer 1

[tiago211287]

I've never done this, but I would try starting looking for the conserved synteny between them. There is a bunch of tools constructed for this purpose. After finding those conserved regions, you could analyze to find the variants. This question has been discussed also here and here.

[kk.mahsa]

thanks but this is not what i want