Dear Respected Experts,

I hope this message finds you well. I am writing to seek your kind guidance regarding an issue I am encountering. I would be extremely grateful for your assistance.

My research focuses on the Orthoptera species Schistocerca gregaria, which I collected from three locations: Kunming, Xi'an, and Yan'an. I am currently estimating the population distances using FST. In my VCF file, the samples are labeled as S_gregaria_Kunming, S_gregaria_Xi'an, and S_gregaria_Yan'an. I merged the data using the bcftools command.

Following the general guidelines provided at the Population Genomics Workshop 5, I used the vcftools command for FST calculation as shown below:

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

For my specific dataset, I adapted the command as follows:                                                                                                                                                                                                            vcftools --vcf all_samples.vcf --weir-fst-pop group_kunming.txt --weir-fst-pop group_xian.txt --weir-fst-pop group_yanan.txt --out pop1_vs_2_vs_3_FST

Here, the text files (group_kunming.txt, group_xian.txt, and group_yanan.txt) list the corresponding sample names as they appear in the VCF file. Despite following these steps, I am encountering -nan values in the output, which has left me confused.

Could you kindly provide guidance or suggest potential solutions to resolve this issue? Your help would mean a great deal to me.

Thank you in advance for your time and support.

Best regards,