As of July 2015, the VCFtools project has been moved to github! Please visit the new website here: vcftools.github.io/links.html
- 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.
- Samtools - a tool 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.