Hi

I have to run this on 136 .vcf files but manually one by one takes an ages 

Can you please help me in any script to do that at the same time in terminal?

    [fi1d18@cyan01 snp]$ bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%ID]\n' file.vcf > file.txt
    [fi1d18@cyan01 snp]$
     

Thanks 
Thank you @genomax

Similar to what you suggested, in terminal one should type

    for f in *.vcf;  bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%ID]\n' "$f" > ${f%.*}.txt done