The Variant Call Format (VCF) is a flat-file, tab-delimited textual format
intended to concisely describe reference-indexed variations between
individuals. VCF provides a common interchange format for the description of
variation in individuals and populations of samples, and has become the defacto
standard reporting format for a wide array of genomic variant detectors.

vcflib provides methods to manipulate and interpret sequence variation as it
can be described by VCF. It is both:

    an API for parsing and operating on records of genomic variation as it can
    be described by the VCF format

    and a collection of command-line utilities for executing complex
    manipulations on VCF files.

The API itself provides a quick and extremely permissive method to read and
write VCF files. Extensions and applications of the library provided in the
included utilities (*.cpp) comprise the vast bulk of the library's utility for
most users.

WWW: https://github.com/vcflib/vcflib