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lge22.vcf nuc.diversity.within value is way too high #5

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gclemd opened this issue May 23, 2019 · 0 comments

gclemd commented May 23, 2019

Hello,
I am running through your examples and no errors but the pi value for your lge22.vcf is
1153, which seems really high.

GENOMEb.class <- readData("/home/popgenome/great_tit/vcf2",format="VCF")
GENOMEb.class_fst <- F_ST.stats(GENOMEb.class)
get.diversity(GENOMEb.class_fst)[[1]] #output:

nuc.diversity.within hap.diversity.within Pi hap.F_ST.vs.all nuc.F_ST.vs.all

#LGE22.vcf 1153.292 1 1153.292 NaN NaN

Do you have a value for this?
Any reason why this is so high? eg what am I doing wrong?
thx

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