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  • extract list ids from a vcf file for Fst calculation

    I would like to calculate Fst from the short-paired reads. For that, I did mapping with minimap2.

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

    # Converted to bam file
    samtools view -Sb aln.sam > aln.bam

    # Sorted the bam file
    samtools sort aln.bam > aln_sorted.bam

    # created an index file of sorted bam
    samtools index aln_sorted.bam

    # created an index file of reference
    samtools faidx ref.fa

    extracted the raw variants using freebayes.
    freebayes -f ref.fa aln_sorted.bam > out_var.vcf

    extracted SNPs using vcf tools
    vcftools --vcf out_var.vcf --remove-indels --recode --recode-INFO-all --out snps_only.vcf

    for getting the ids from the vcf file for Fst calculation, I used bcf tools

    bcftools query -l snps_only.vcf

    I got the output​ `unknown`. How to retrieve the list ids? your suggestions would be appreciated.

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