- 1000 Genomes Project main page
- The Genome Analysis Toolkit - The GATK Java package from the Broad includes a number of routines for generating and manipulating VCF file.
- HTSlib - a toolset that can generate VCF files from SAM or BAM format files
- Tabix - an indexing tool that is required for certain features in the PERL API.
- vcflib - A simple C++ library for parsing and manipulating VCF files from Erik Garrison.
- VcfPythonUtils - Some Python utilities to work with VCF from Amit Indap.
- vcfCTools - C++ implementation of vcfPytools from Alistair Ward.