How I can change the name of multiple files at once in R or terminal?
Use perl-rename. This is usually called rename on Debian-based systems like Ubuntu or Mint, and perl-rename or prename on others. Assuming you have it as rename, you can simply do:

rename -n 's/.*\.vcf/"A" . ++$c . ".vcf"/e' *snp.pass.vcf


The -n causes rename to only print what it would do, without doing anything. So once you make sure it does what you want, run the command again without the -n.