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A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
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README.md

VCFtools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Project website: https://vcftools.github.io/

License

The program package is released under the GNU Lesser General Public License version 3.0 (LGPLv3). See the LICENSE file for the complete LGPL license text.

Credits

  • Adam Auton (Binary Executable)
  • Petr Danecek (Perl Module)
  • Anthony Marcketta (Binary Executable)

Building VCFtools

General help about the building process's configuration step can be acquired via:

./configure --help

Build from Release Tarball

./configure
make
make install

You may need sudo permissions to run make install.

Build from GitHub

git clone https://github.com/vcftools/vcftools.git
cd vcftools
./autogen.sh
./configure
make
make install

You many need sudo permissions to run make install.

Documentation

Documentation and usage examples can be found here:

https://vcftools.github.io/examples.html

A manual page is also available. If prefix is set to /usr or if MANPATH points to $prefix/share/man, you can access the manual page via:

man vcftools

Getting Help

The best way to get help regarding VCFtools is to email the mailing list:

vcftools-help@lists.sourceforge.net

Citation

If you make use of VCFtools in your research, we would appreciate a citation of the following paper:

The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011 http://dx.doi.org/10.1093/bioinformatics/btr330

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