Fst

Fst

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Master command
--fst
It reads in the subgroup of the individuals. The format for fat.cls reads three columns, family ID, individual ID, and sub-population id

FID1     IID1     Sub1
FID2     IID2     Sub2
…
FID100     IID100     Sub100

Example

gear --fst id.cls --bfile test --out test

The output, for example, for two sub populations reads

Chr	SNP	Pos	RefA	prop1	Freq1	NInd1	prop2	Freq2	NInd2	Freq	Fst
1	rs0	0	A	0.5	1.0	500	0.5	0.0	500	0.5	1.0