[Vcftools-help] Fst results: nan

[Katie C. <kjc...@gm...>]

I am trying to calculate Fst on two populations: 1 has 5 individuals, the other has 12.  It appears as the Fst for every position is nan.  Could it be because of missing genotypes?  I attached a portion of the vcf file.

Here is a screen shot of my terminal:

vcftools --vcf ~/Desktop/OakVin2.recode.vcf --out ~/Desktop/OakVinFst --weir-fst-pop ~/Desktop/VinList.txt --weir-fst-pop ~/Desktop/OakList.txt

VCFtools - v0.1.12a
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
	--vcf /Users/clowers/Desktop/OakVin2.recode.vcf
	--weir-fst-pop /Users/clowers/Desktop/VinList.txt
	--weir-fst-pop /Users/clowers/Desktop/OakList.txt
	--out /Users/clowers/Desktop/OakVinFst

After filtering, kept 17 out of 17 Individuals
Outputting Weir and Cockerham Fst estimates.
Weir and Cockerham mean Fst estimate: nan
Weir and Cockerham weighted Fst estimate: nan
After filtering, kept 370792 out of a possible 370792 Sites
Run Time = 18.00 seconds