Converting VCF file to PLINK bed/bim/fam files
Given that Plink reads in VCF files natively, and Plink is your desired output format, I expect that plink --vcf &lt;file&gt; would be the best option.

There are caveats associated with the types of variants that Plink will pull in from the VCF files, mostly related to limitations of Plink's own file formats. But if your end-goal is Plink, then that should be fine.