FST Calculation: Resolving -nan Issue in Population Genetics Analysis

Question

[hashim.rana11]

I have a sample of a species, with data from three different locations. I have calculated its nucleotide diversity and Tajima's D, but when I calculate FST (estimating population distance with FST), it shows -nan.

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vcftools --vcf all_samples.vcf --weir-fst-pop Population_1_ethiopia_names --weir-fst-pop Population_2_ethiopia_names --out pop1_vs_2_FST

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Is there any solution for this? Has anyone calculated it in this way? Please guide me about this. Thanks in advance and I am waiting your answers. Best regards,

[Michael]

This should work. I would check if the names in the population files are correct and are actually the correct sample names present in the vcf file. Try bcftools query -l to get the sample names and compare. Another issue I would check is if there are any variable positions at all between the groups (though that should give 0) and that the ploidy is <= 2.