I know most of you would suggest me to use either `bedtool` or `bcftools`, but I tried  a lot with these but could not get full information in my subset vcf file where I intend to extract the SNPs with all column information and updated `AC`, `DP` values etc. in `my_bed.bed` file. When I tried this with `bedtool`, I couldn't process the file due to conflicting AC= column values (it does not change in the subset data), So I am trying to get this done using `vcftools`. However, `vcftools` is also not immune to this problem as I am still missing most of the `FORMAT` column information (`AC=0;AF=0.00054;AN=312;BaseQRankSum=-2.079;DP=40153;Dels=0.00;FS=1.621;HRun=0;HaplotypeScore=0.2550`)

The command I am using to extract using vcftool is :

    for file in *.vcf.gz; do
    vcftools --gzvcf $file --recode --recode-INFO-all --bed /dir_for_bed_file/my_bed.bed --out  "${file}".vcf
    done

Can someone please clarify the fuss here or if I am missing anything in my command line?
Ok figured it out: It was missing `--recode --recode-INFO-all`.  