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<h1>Table Of Contents<a class="headerlink" href="#table-of-contents" title="Permalink to this headline">ΒΆ</a></h1>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="overview.html">Overview</a><ul>
<li class="toctree-l2"><a class="reference internal" href="overview.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#rtg-software-description">RTG software description</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#installation-and-deployment">Installation and deployment</a><ul>
<li class="toctree-l3"><a class="reference internal" href="overview.html#quick-start-instructions">Quick start instructions</a></li>
<li class="toctree-l3"><a class="reference internal" href="overview.html#license-management">License Management</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#technical-assistance-and-support">Technical assistance and support</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="rtg_command_reference.html">RTG Command Reference</a><ul>
<li class="toctree-l2"><a class="reference internal" href="rtg_command_reference.html#command-line-interface-cli">Command line interface (CLI)</a></li>
<li class="toctree-l2"><a class="reference internal" href="rtg_command_reference.html#rtg-command-syntax">RTG command syntax</a></li>
<li class="toctree-l2"><a class="reference internal" href="rtg_command_reference.html#data-formatting-commands">Data Formatting Commands</a><ul>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#format">format</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#sdf2fasta">sdf2fasta</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#sdf2fastq">sdf2fastq</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#sdf2sam">sdf2sam</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#fastqtrim">fastqtrim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#petrim">petrim</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="rtg_command_reference.html#simulation-commands">Simulation Commands</a><ul>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#genomesim">genomesim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#cgsim">cgsim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#readsim">readsim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#popsim">popsim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#samplesim">samplesim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#denovosim">denovosim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#childsim">childsim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#pedsamplesim">pedsamplesim</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#samplereplay">samplereplay</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="rtg_command_reference.html#utility-commands">Utility Commands</a><ul>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#bgzip">bgzip</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#index">index</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#extract">extract</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#aview">aview</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#sdfstats">sdfstats</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#sdfsubset">sdfsubset</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#sdfsubseq">sdfsubseq</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#mendelian">mendelian</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcfannotate">vcfannotate</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcfdecompose">vcfdecompose</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcfeval">vcfeval</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcffilter">vcffilter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcfmerge">vcfmerge</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcfsplit">vcfsplit</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcfstats">vcfstats</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcfsubset">vcfsubset</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#vcf2rocplot">vcf2rocplot</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#svdecompose">svdecompose</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#bndeval">bndeval</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#pedfilter">pedfilter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#pedstats">pedstats</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#rocplot">rocplot</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#version">version</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#license">license</a></li>
<li class="toctree-l3"><a class="reference internal" href="rtg_command_reference.html#help">help</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="administration.html">Administration & Capacity Planning</a><ul>
<li class="toctree-l2"><a class="reference internal" href="administration.html#advanced-installation-configuration">Advanced installation configuration</a></li>
<li class="toctree-l2"><a class="reference internal" href="administration.html#run-time-performance-optimization">Run-time performance optimization</a></li>
<li class="toctree-l2"><a class="reference internal" href="administration.html#alternate-configurations">Alternate configurations</a></li>
<li class="toctree-l2"><a class="reference internal" href="administration.html#exception-management-talkback-and-log-file">Exception management - TalkBack and log file</a></li>
<li class="toctree-l2"><a class="reference internal" href="administration.html#usage-logging">Usage logging</a><ul>
<li class="toctree-l3"><a class="reference internal" href="administration.html#single-user-single-machine">Single-user, single machine</a></li>
<li class="toctree-l3"><a class="reference internal" href="administration.html#multi-user-or-multiple-machines">Multi-user or multiple machines</a></li>
<li class="toctree-l3"><a class="reference internal" href="administration.html#advanced-usage-configuration">Advanced usage configuration</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="administration.html#command-line-color-highlighting">Command-line color highlighting</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="appendix.html">Appendix</a><ul>
<li class="toctree-l2"><a class="reference internal" href="appendix.html#rtg-reference-file-format">RTG reference file format</a></li>
<li class="toctree-l2"><a class="reference internal" href="appendix.html#pedigree-ped-input-file-format">Pedigree PED input file format</a></li>
<li class="toctree-l2"><a class="reference internal" href="appendix.html#genetic-map-directory">Genetic map directory</a></li>
<li class="toctree-l2"><a class="reference internal" href="appendix.html#rtg-commands-using-indexed-input-files">RTG commands using indexed input files</a></li>
<li class="toctree-l2"><a class="reference internal" href="appendix.html#rtg-javascript-filtering-api">RTG JavaScript filtering API</a><ul>
<li class="toctree-l3"><a class="reference internal" href="appendix.html#vcf-record-field-access">VCF record field access</a></li>
<li class="toctree-l3"><a class="reference internal" href="appendix.html#vcf-record-modification">VCF record modification</a></li>
<li class="toctree-l3"><a class="reference internal" href="appendix.html#vcf-header-modification">VCF header modification</a></li>
<li class="toctree-l3"><a class="reference internal" href="appendix.html#testing-for-overlap-with-genomic-regions">Testing for overlap with genomic regions</a></li>
<li class="toctree-l3"><a class="reference internal" href="appendix.html#additional-information-and-functions">Additional information and functions</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="appendix.html#distribution-contents">Distribution Contents</a></li>
<li class="toctree-l2"><a class="reference internal" href="appendix.html#readme-txt">README.txt</a></li>
<li class="toctree-l2"><a class="reference internal" href="appendix.html#notice">Notice</a></li>
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