Hello. Everyone.

I have been calculating Fst of my sequencing result obtained from RADseq.

I've done variant calling using GATK and finished filtering step of some procedures with vcftools.

Anyhow, I made final vcf file having 138 variants.

I just wanted to know Fst between two different populations in that vcf file, and tried to gain the value using vcftools.

I ran the following command;

vcftools --gzvcf $in/FIN.vcf.gz --weir-fst-pop $pop/A.txt --weir-fst-pop $pop/B.txt --fst-window-size 10000 --out $pop/A-B

After that, I saw a results of something weird.

Using zlib version: 1.2.11

Warning: Expected at least 2 parts in FORMAT entry: ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

Keeping individuals in 'keep' list

After filtering, kept 20 out of 182 Individuals

Outputting Windowed Weir and Cockerham Fst estimates.

Weir and Cockerham mean Fst estimate: -nan

Weir and Cockerham weighted Fst estimate: -nan

After filtering, kept 168 out of a possible 168 Sites

Run Time = 0.00 seconds

Mean Fst and weighted Fst were all 'NaN'.

Have you ever seen this problem?

Although I have been searching to solve this problem and trying to modify based on the vcftools manual, I am still in fog.

If you guys know the way to breakthrough this problem, please be my light.

Thank you!