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ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
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The value of Fst is negative #91

Closed ShirelyI closed 9 months ago

ShirelyI commented 9 months ago

Describe the problem you are having A clear and concise description of what problem you are encountering. 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 commented 9 months ago

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 commented 9 months ago

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