A set of tools written in Perl and C++ for working with VCF files.

VCF (Variant Call Format) specifications

The VCF specification is now maintained by Global Alliance for Genomics and Health Data Working group file format team.

The main version of the VCF specification can be found on github.

A PDF of the (current) v4.2 spec can be found here.
A PDF of the (older) v4.1 spec is available here.