Need help with FST calculation (not homework)

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SUMMARY

The FST estimator is a critical tool for measuring genetic differentiation between populations, with the original formula by Wright now replaced by the more accurate FST estimate introduced by Cockerham and Weir in 1984. The study by Weir and Cockerham, titled "Estimating f-statistics for the analysis of population structure," is essential for understanding this advanced methodology. Recent research has utilized large datasets of SNPs to calculate FST distances among various populations, including significant studies on European and East Asian groups. BioPerl offers freely available FST modules that can assist in these calculations.

PREREQUISITES
  • Understanding of FST calculations and genetic differentiation
  • Familiarity with population genetics concepts
  • Knowledge of SNPs (Single Nucleotide Polymorphisms)
  • Experience with BioPerl and its modules
NEXT STEPS
  • Review the original study by Weir and Cockerham (1984) for foundational knowledge
  • Explore the latest research on FST distances in human populations, particularly the Heath (2008) study
  • Learn how to implement FST calculations using BioPerl modules
  • Investigate algorithms derived from the Weir and Cockerham methodology in various software packages
USEFUL FOR

This discussion is beneficial for population geneticists, bioinformaticians, and researchers interested in genetic diversity and population structure analysis.

argiedude
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Hi, to all. The FST estimator can tell how different 2 populations are, genetically. The normal FST formula was introduced by Wright and can be found very easily, for example, in wikipedia. But it had some flaws, so it's use has now been completely replaced by the FST estimate introduced by Cockerham and Weir (1984). I've tried very hard to find this formula, but I can't.

This is the original study (it's not public access):

B. S. Weir and C. C. Cockerham.
Estimating f-statistics for the analysis of population structure
Evolution, 38:1358-1370, 1984

Recent studies, using 100,000's of mutations in the human dna (SNPs), have produced tables of FST distances between several populations. So far this has been done for several European populations (Heath, 2008), and just a few weeks ago a new study came out which included an FST comparison between 20 East Asian populations.

It's all extremely interesting. Here's a graph I made of the genetic distances from the Heath study:

FST-autosomalEuropeHeath2008.gif


Can you help?
 
Biology news on Phys.org
https://en.wikipedia.org/wiki/Fixation_index FST modules are freely available in BioPerl for example.
Someone else may know precisely which algorithms (and in what software packages) are derived from Weir and Cockerham.
 
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