So I am a beginner in Plink, I have a dataset of 6 individuals (SNP data in autosomes genome-wide, so over 100M SNPs). I would like to see if there is any kind of group forming/clusters (because some are wild and some are captive born).
I have been trying to solve this using IBS in Plink 1.9. However, they will all cluster together in one cluster. If I use the option to determine the amount of individuals allowed per cluster (and I set this to three) I get of course two clusters, one with wild and one with captive individuals, but I think this is purely because they are also ordered as such in the input file (and not necessarily because they cluster together).
I have also data on 32 individuals of other closely related species and I wanted to check whether using IBS would indeed cluster different species at least into different cluster, but again all my 38 individuals cluster in one and the same cluster.
So my question actually is whether anyone here has experience with using IBS and making it more 'strict' in some sort of way so that I can still get different groups out of it. I am not sure how I can make my IBS clustering more strict (if you know what I mean...).
Sorry for the long post! Any help is much appreciated :)