Post by Jian Yang on Jun 10, 2015 5:01:58 GMT
Calculating Fst following the method described in Weir (1996).
Example
Format of input file ("subpopu.txt")
Output
Results are saved in *.fst file.
References
Fst method: Weir, B.S. 1996. Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates, Inc. Sunderland, Massachusetts.
GCTA software: Yang J, Lee SH, Goddard ME and Visscher PM. (2011) GCTA: a tool for Genome-wide Complex Trait Analysis. Am J Hum Genet, 88: 76-82. [PubMed ID: 21167468]
Example
gcta64 --bfile test --fst --sub-popu subpopu.txt --out testFormat of input file ("subpopu.txt")
1 11 Popu1
2 21 Popu1
3 31 Popu2
4 41 Popu2
5 51 Popu1
6 61 Popu2
...Output
Results are saved in *.fst file.
Chr SNP bp refA freq_Popu1(n=1000) freq_Popu2(n=2925) Fst
1 rs4475691 836671 T 0.208561 0.193984 0.000508832
1 rs28705211 890368 C 0.287427 0.274928 0.000295543
1 rs9777703 918699 C 0.0265765 0.0313871 0.000300492
...
References
Fst method: Weir, B.S. 1996. Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates, Inc. Sunderland, Massachusetts.
GCTA software: Yang J, Lee SH, Goddard ME and Visscher PM. (2011) GCTA: a tool for Genome-wide Complex Trait Analysis. Am J Hum Genet, 88: 76-82. [PubMed ID: 21167468]