index.html

---
layout: default
---

<div class="well homepage-intro">
	<h1>Samtools</h1>
	<p>Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:</p>
	
	<dl class="dl-horizontal">
		<dt>Samtools</dt>
		<dd>Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format</dd>
		
		<dt>BCFtools</dt>
		<dd>Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants</dd>
		
		<dt>HTSlib</dt>
		<dd>A C library for reading/writing high-throughput sequencing data</dd>
	</dl>
	
	<p>Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.</p>
	
</div>

<div class="row home-boxes">
	<div class="col-lg-3 col-sm-6">
		<div class="well">
			<h3><a href="{{ "/download" | relative_url }}"><i class="glyphicon glyphicon-save"></i> Download</a></h3>
			<p>Source code releases can be downloaded from&nbsp;<a href="https://github.com/samtools/">GitHub</a>
			or&nbsp;<a href="http://sourceforge.net/projects/samtools/files/samtools/">Sourceforge</a>:</p>
			<a class="btn btn-primary btn-lg" href="{{ "/download" |relative_url }}"><i class="glyphicon glyphicon-cloud-download"></i>&emsp;Source release details</a>
		</div>
	</div>
	<div class="col-lg-3 col-sm-6">
		<div class="well">
			<h3><a href="{{ "/workflow" | relative_url }}"><i class="glyphicon glyphicon-transfer"></i> Workflows</a></h3>
			<p>We have described some standard workflows using Samtools:</p>
			<ul>
				<li><a href="{{ "/workflow/fastq.html" | relative_url }}">FASTQ to BAM / CRAM</a></li>
				<li><a href="{{ "/workflow/wgs-call.html" | relative_url }}">WGS/WES Mapping to Variant Calls</a></li>
				<li><a href="{{ "/workflow/filter.html" | relative_url }}">Filtering of VCF Files</a></li>
				<li><a href="{{ "/workflow/cram.html" | relative_url }}">Using CRAM within Samtools</a></li>
			</ul>
		</div>
	</div>
	
	<div class="clearfix visible-md-block visible-sm-block"></div>
	
	<div class="col-lg-3 col-sm-6">
		<div class="well">
			<h3><a href="{{ "/doc" | relative_url }}" ><i class="glyphicon glyphicon-list-alt"></i> Documentation</a></h3>
			<ul>
				<li><a href="{{ "/doc#manual-pages" | relative_url }}">Manuals</a></li>
				<li><a href="{{ "/doc#howtos" | relative_url }}">HowTos</a></li>
				<li><a href="{{ "/doc#file-formats" | relative_url }}">Specifications</a></li>
				<li><a href="{{ "/algorithms/duplicate.html" | relative_url }}">Duplicate Marking</a></li>
				<li><a href="{{ "/benchmarks/zlib.html" | relative_url }}">Zlib Benchmarks</a></li>
				<li><a href="{{ "/benchmarks/CRAM.html" | relative_url }}">CRAM Benchmarks</a></li>
				<li><a href="{{ "/doc#publications" | relative_url }}">Publications</a></li>
			</ul>
		</div>
	</div>
	<div class="col-lg-3 col-sm-6">
		<div class="well">
			<h3><a href="{{ "/support" | relative_url }}"><i class="glyphicon glyphicon-question-sign"></i> Support</a></h3>
			<ul>
				<li><a href="{{ "/support#lists" | relative_url }}">Mailing Lists</a></li>
				<li><a href="https://github.com/samtools/htslib/issues">HTSlib issues</a></li>
				<li><a href="https://github.com/samtools/bcftools/issues">BCFtools issues</a></li>
				<li><a href="https://github.com/samtools/samtools/issues">Samtools issues</a></li>
			</ul>
		</div>
	</div>
</div>