Question: Fst between the combination of populations (pairwise)
0
gravatar for cmcouto.silva
2.3 years ago by
São Paulo, Brazil.
cmcouto.silva30 wrote:

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,

plink fst pairwise • 1.8k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by cmcouto.silva30
2

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.

ADD REPLYlink written 2.2 years ago by chrchang5237.3k

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

Best Regards,

ADD REPLYlink written 2.2 years ago by cmcouto.silva30
1

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by h.mon31k
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