Fst - gc5k/GEAR GitHub Wiki
Fst statistic is commonly used for quantifying population structure with a prior for grouping.
The early credit of constructing Fst should go to
- Sewall Wright, The genetical structure of populations, Annals of Eugentics, 1951, 15:323-54
- Clark Cockerham, The analyses of gene frequencies, Genetics, 1973, 74:679-700
and it was matured and widely accepted since the work below
- Bruce Weir & Clark Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, 1984, 1358-70
A recent comprehensive discussion of Fst can be found by
- Gaurav Bhatia, Nick Patterson, Sriram Sankararaman, et al., Estimating and interpreting Fst: the impact of rare variants, Genome Research, 2013, 23:1514-21
Master command: fst
options
--bfile
Specify the binary genotype data.
--group
Specify the grouping of the population. A typical group file has three mandatory columns: family id, individual id, and group, respectively. It may read as below (no title line)
| family ID | individual ID | group |
|---|---|---|
| CEU | Ind1 | 1 |
| CEU | Ind2 | 1 |
| CHB | Ind1 | 1 |
| CHB | Ind2 | 1 |
Examples
java -jar gear.jar fst --bfile test --group test.txt --out test