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tools.html
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<!DOCTYPE html>
<html>
<head>
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
<meta name="google-site-verification" content="7eDjHMCU1NQK0HwCiHV-Y6E9pfOe8JkAc49dcdl3mWc" />
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>AML31 Supplementary Information</title>
<link rel="shortcut icon" href="http://genome.wustl.edu/workspace/images/favicon.ico" type="image/x-icon" />
<link rel="stylesheet" type="text/css" href="main.css" />
</head>
<body class="home">
<div class="navbar">
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<div class="row helix">
<img src="tgi_logo_shadow.png" title="The McDonnell Genome Institute at Washington Unversity School of Medicine" alt="The McDonnell Genome Institute at Washington Unversity School of Medicine" style="float:left;margin-left:25px;"/>
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<div class="nav-collapse">
<ul class="nav">
<li>
<a href="index.html">Main</a>
</li>
<li>
<a href="sequence.html">Sequence Data</a>
</li>
<li>
<a href="methods.html">Methods</a>
</li>
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<a href="analyses.html">Analyses</a>
</li>
<li>
<a href="tools.html">Tools</a>
</li>
<li>
<a href="citation.html">Citation</a>
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<div class="container background">
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<div class="aml31span4 main-block projects">
<div class="block-padding">
<h2 class="heading">Tools</h2>
<div class="content">
<ul class="analysislist">
<li><a href="https://github.com/genome/aml31Benchmarking">R package for easy benchmarking of variant calls against the platinum and gold lists</a></li>
</ul>
<h3>Selected tools used in this publication</h3>
<ul>
<li><a href="https://github.com/genome/sciclone">sciClone</a></li>
<li><a href="https://github.com/hdng/clonevol">CloneEvol</a></li>
<li><a href="http://tvap.genome.wustl.edu/tools/bassovac/">Bassovac</a></li>
<li><a href="https://www.broadinstitute.org/cancer/cga/MuTect">Mutect</a></li>
<li><a href="http://gmt.genome.wustl.edu/packages/somatic-sniper/">Somatic Sniper</a></li>
<li><a href="https://sites.google.com/site/seuratsomatic/">Seurat</a></li>
<li><a href="http://varscan.sourceforge.net/">VarScan</a></li>
<li><a href="https://sites.google.com/site/strelkasomaticvariantcaller/">Strelka</a></li>
<li><a href="https://github.com/nhansen/Shimmer/">Shimmer</a></li>
<li><a href="https://github.com/chrisamiller/copycat">CopyCat</a></li>
<li><a href="http://bio-bwa.sourceforge.net/">BWA</a></li>
<li><a href="https://www.sanger.ac.uk/resources/software/smalt/">SMALT</a></li>
<li><a href="http://snap.cs.berkeley.edu/">SNAP</a></li>
<li><a href="http://www.well.ox.ac.uk/project-stampy">Stampy</a></li>
<li><a href="https://github.com/sequencing/isaac_aligner">Isaac</a></li>
<li><a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml">Bowtie2</a></li>
</ul>
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</a>
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<a href="http://en.wikipedia.org/wiki/The_Genome_Institute">
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Copyright © 1993-2014 Washington University in St. Louis. All rights reserved.
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<a href="http://medschool.wustl.edu/">
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</a>
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</html>