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https://github.com/vcftools/vcftools
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
https://github.com/vcftools/vcftools
Last synced: 13 days ago
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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.
- Host: GitHub
- URL: https://github.com/vcftools/vcftools
- Owner: vcftools
- License: lgpl-3.0
- Created: 2015-06-25T13:48:11.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2023-11-17T09:53:37.000Z (12 months ago)
- Last Synced: 2024-07-31T22:49:48.844Z (3 months ago)
- Language: C++
- Homepage: https://vcftools.github.io/
- Size: 851 KB
- Stars: 489
- Watchers: 33
- Forks: 149
- Open Issues: 113
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- Awesome-Bioinformatics - vcftools - VCF manipulation and statistics (e.g. linkage disequilibrium, allele frequency, Fst). [ [paper-2011](https://pubmed.ncbi.nlm.nih.gov/21653522) ] (Next Generation Sequencing / VCF File Utilities)
- awesome-genetics - vcftools/vcftools
README
# VCFtools
A set of tools written in Perl and C++ for working with [VCF files](https://samtools.github.io/hts-specs/VCFv4.2.pdf), such as those generated by the
[1000 Genomes Project](http://www.1000genomes.org/).
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:
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