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?