Fst calculation from VCF files

Question

I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and SNPs_s4.vcf, which contain information about SNPs. These vcf files were obtained by using the following methods: the initial input files were short-paired reads

1. I did mapping with minimap2

   ./minimap2 -ax sr ref.fa read1.fq.gz read2.fq.gz > aln.sam
   

2. converted to bam file

   samtools view -Sb aln.sam > aln.bam
   

3. Sorted the bam file

   samtools sort aln.bam > aln_sorted.bam
   

4. created an index file

   samtools index aln_sorted.bam
   

5. created an index file of reference

   samtools faidx ref.fa
   

6. extracted the raw variants using freebayes

   freebayes -f ref.fa aln_sorted.bam > out_var_s1.vcf
   

7. extracted SNPs using vcf tools

   vcftools --vcf out_var_s1.vcf --remove-indels --recode \
      --recode-INFO-all --out SNPs_s1.vcf
   

I would like to calculate the fixation index (Fst) between SNPs_s1.vcf and SNPs_s2.vcf, SNPs_s1.vcf and SNPs_s3.vcf etc. I attempted to calculate Fst using bcftools, but I have to provide the id list. I tried the code below for that.

bcftools query -l snps_s1.vcf

The output was "unknown".

How do I calculate Fst using the above vcf files? Your suggestions would be appreciated.