I need to get Fst values for multiple populations combined pairwisely.
Populations: Pop1 Pop2 Pop3 Pop4 Pop5
Pop1 with Pop2 Pop1 with Pop3 Pop1 with Pop4 Pop1 with Pop5 Pop2 with Pop3 Pop2 with Pop4 Pop2 with Pop5 Pop3 with Pop4 Pop3 with Pop5 Pop4 with Pop5
I am using the raw/weighted mean provided in the log information from Plink Software.
I know I can compare Fst among multiple populations using a cluster in Plink, but it returns a single value for all considered populations, and I would like to get a value for each combination.
I did a script with that purpose, but as long as I have 62 population, there are 1891 combinations, so that I'm running plink 1891 times and getting a total of 5673 files (for each running, three files have been generated: .fst, .log, and .nosex).
I wonder if there is a method in plink to consider the combination between the groups in a cluster instead of them all together.
Thanks in advance,