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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<title>VCFtools</title>
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<body>
<div class="wrapper">
<header>
<h1 class="header">VCFtools</h1>
<p class="header">A set of tools written in Perl and C++ for working with VCF files.</p>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="examples.html">Documentation</a></li>
<li class="download"><a class="buttons" href="https://github.com/vcftools/vcftools/zipball/master">Download ZIP</a></li>
<li class="download"><a class="buttons" href="https://github.com/vcftools/vcftools/tarball/master">Download TAR</a></li>
<li><a class="buttons github" href="https://github.com/vcftools/vcftools">View On GitHub</a></li>
</ul>
</header>
<section>
<h2>
<a id="welcome-to-vcftools" class="anchor" href="#welcome-to-vcftools" aria-hidden="true"><span class="octicon octicon-link"></span></a>Welcome to VCFtools</h2>
<p><strong>VCFtools</strong> is a program package designed for working with VCF files, such as those generated by the <a href="http://www.1000genomes.org/">1000 Genomes Project</a>.
The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.</p>
<p>This toolset can be used to perform the following operations on VCF files:
<ul>
<li>Filter out specific variants</li>
<li>Compare files</li>
<li>Summarize variants</li>
<li>Convert to different file types</li>
<li>Validate and merge files</li>
<li>Create intersections and subsets of variants</li>
</ul>
</p>
<p>VCFtools consists of two parts, a <strong>perl module</strong> and a <strong>binary executable</strong>. The perl module is a general Perl API for manipulating VCF files, whereas the binary executable provides general analysis routines.
</p>
<h2>Download</h2>
<p>To obtain VCFtools, please visit the <a href="downloads.html">downloads</a> page.</p>
<h2>Variant call format specification</h2>
<p>VCFtools is compatible with VCF versions 4.0, 4.1 and 4.2. For more information regarding the VCF format, please visit the <a href="specs.html">VCF specification page</a>.</p>
<h2>Contact</h2>
<p>For help regarding VCFtools or the VCF format, please see the <a href="http://sourceforge.net/p/vcftools/mailman/"> mailing lists</a>.</p>
<h2>Citations and Licensing</h2>
<p>Information about licensing and publications can be found <a href="license.html">here</a>.</p>
<h2>Links</h2>
<p>Other useful links can be found on <a href="links.html">this</a> page.</p>
</section>
<footer>
<p><small>Hosted on <a href="https://pages.github.com">GitHub Pages</a></small></p>
<p>Copyright 2015 © VCFtools</p>
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