I generated a VCF file including 20 samples belonging to two species (A and B), variant calling was done using GATK best practice pipeline (only autosomes chromosomes). Now I want to detect the introgressed regions from A sp. to B sp. I searched for a way to do that and find more articles used the ABBA BABA test and fd statistics. When I read some articles and some manuals for this test, I found they use 4 populations (P1, P2, P3, and O as outgroup).
Now my question is, how I can handle this analysis using two populations?
Do you have a suggestion for another valid method of identifying introgressed regions?