Fst between the combination of populations (pairwise)

Question

[cmcouto.silva]

Hello everyone!

I need to get Fst values for multiple populations combined pairwisely.

__For example:__

---

Populations: Pop1 Pop2 Pop3 Pop4 Pop5

Combinations:

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,
Best,

[chrchang523]

No, this isn't built into plink 1.9, so something like your script is currently necessary. I'll plan on adding a way to do this in plink 2.0's --fst implementation, though.

[cmcouto.silva]

Glad to know that! Thanks for both of your answers!

Best Regards,

[h.mon]

At least a few years ago, there wasn't. Tagging chrchang523 in case he missed your question.

edit: other relevant posts

https://groups.google.com/forum/#!topic/plink2-users/h81FEBhIwRw

Calculating statistically significant outlier for Pairwise Fst obtained from VCFTools