Fst between the combination of populations (pairwise)
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3.5 years ago

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 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.

Best,

fst pairwise plink • 2.9k views
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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.

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Best Regards,

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