The value of Fst is negative

[ShirelyI]

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The value of Fst is negative

Hi Kieran,
After I calculated the Fst I found some value of Fst was negative. Do you know how to deal with these values?
For I want to transform per SNP FST with a Z transformation normalized across the chromosomes, and the ZFst also contain negative values, I noticed in other papers that Fst or ZFst are always greater than 0, do you know what should I do with those negative values?
Best,
Lily

[ksamuk]

Hi Lily,

Weir and Cockerham's FST can be negative. This is often the case in populations with low differentiation. I've never seen the implications of this fully explored, but it is common to see people set negative FSTs to zero prior to analysis. Hudson's FST is also available via --fst_type hudson.

Hope that helps,

Kieran

[ShirelyI]

Hi Kieran,
yes you're right, thanks for your help.
Best,
Lily