Whole-exome and whole-genome sequencing also enables detailed study of structural variations which defy clean representation under a single coordinate system; and the number of individuals in such studies is typically much smaller than the tens or even hundreds of thousands which are sometimes required for effective GWAS. There are no plans to make PLINK suitable for this type of analysis; we strongly recommend the use of another software package, such as PLINK/SEQ [45], which is explicitly designed for it. This is why the PLINK 2 file format will still be substantially less expressive than VCF.
