As of July 2015, the VCFtools project has been moved to github! Please visit the new website here:

Useful Links

  • 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.