Converting VCF file to PLINK bed/bim/fam files I am trying to find the best way to convert VCF files to PLINK binary bed/bim/fam files, but it seems like there are many varied ways to do this. (For example, using Plink 1.9 --vcf tag, bcftools, GATK, and vcftools). 

Obviously they all probably have their uses and you could likely spend a while discussing this, but can anyone give a short, simple explanation as to whether the methods are generally the same, or whether one or another is generally best for certain situations? Thanks!
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.