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<li class="toctree-l1 current"><a class="current reference internal" href="#">RADSex usage</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#process">process</a></li>
<li class="toctree-l2"><a class="reference internal" href="#distrib">distrib</a></li>
<li class="toctree-l2"><a class="reference internal" href="#signif">signif</a></li>
<li class="toctree-l2"><a class="reference internal" href="#map">map</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#subset">subset</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#freq">freq</a></li>
<li class="toctree-l2"><a class="reference internal" href="#depth">depth</a></li>
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  <div class="section" id="radsex-usage">
<span id="full-usage"></span><h1>RADSex usage<a class="headerlink" href="#radsex-usage" title="Permalink to this headline"></a></h1>
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<p>The RADSex software implements the general command-line interface:</p>
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<p><code class="docutils literal notranslate"><span class="pre">radsex</span> <span class="pre">&lt;command&gt;</span> <span class="pre">[options]</span></code></p>
<p><strong>Available commands</strong></p>
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<table class="docutils align-default">
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<colgroup>
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<thead>
<tr class="row-odd"><th class="head"><p>Command</p></th>
<th class="head"><p>Description</p></th>
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</tr>
</thead>
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<tbody>
<tr class="row-even"><td><p>depth</p></td>
<td><p>Compute marker depth statistics for each individual</p></td>
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</tr>
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<tr class="row-odd"><td><p>distrib</p></td>
<td><p>Compute the distribution of markers between compared groups</p></td>
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</tr>
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<tr class="row-even"><td><p>freq</p></td>
<td><p>Compute the distribution of markers in all individuals</p></td>
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</tr>
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<tr class="row-odd"><td><p>map</p></td>
<td><p>Align markers to a genome and compute metrics for each aligned marker</p></td>
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</tr>
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<tr class="row-even"><td><p>process</p></td>
<td><p>Compute a table of marker depths from a set of demultiplexed reads files</p></td>
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</tr>
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<tr class="row-odd"><td><p>signif</p></td>
<td><p>Extract markers significantly associated with phenotypic group from a marker depths table</p></td>
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</tr>
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<tr class="row-even"><td><p>subset</p></td>
<td><p>Extract a subset of markers from a marker depths table</p></td>
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</tr>
</tbody>
</table>
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<hr class="docutils" />
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<div class="section" id="process">
<span id="process-usage"></span><h2>process<a class="headerlink" href="#process" title="Permalink to this headline"></a></h2>
<p>Generate a table containing the depth of each marker in each individual from the dataset.</p>
<p><strong>Command</strong></p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">radsex</span> <span class="n">process</span> <span class="o">--</span><span class="nb">input</span><span class="o">-</span><span class="nb">dir</span> <span class="n">input_dir_path</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">file</span> <span class="n">output_file_path</span> <span class="p">[</span> <span class="o">--</span><span class="n">threads</span> <span class="n">n_threads</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">depth</span> <span class="n">min_depth</span> <span class="p">]</span>
</pre></div>
</div>
<p><strong>Options</strong></p>
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<table class="docutils align-default">
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<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
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</tr>
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<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--input-dir,</span> <span class="pre">-i</span></code></p></td>
<td><p>Path to a folder containing demultiplexed reads</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the generated marker depths table</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--threads,</span> <span class="pre">-T</span></code></p></td>
<td><p>Number of threads to use (default: 1)</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></p></td>
<td><p>Minimum depth to consider a marker present in an individual (default: 1)</p></td>
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</tr>
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</table>
<p><strong>Output</strong></p>
<p>A <a class="reference internal" href="output_files.html#markers-depths-table-file"><span class="std std-ref">Markers depth table</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">#Number of markers : 4</span>
<span class="nb">id</span>   <span class="n">sequence</span>     <span class="n">individual_1</span>    <span class="n">individual_2</span>    <span class="n">individual_3</span>    <span class="n">individual_4</span>    <span class="n">individual_5</span>
 <span class="mi">0</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">TATT</span>              <span class="mi">0</span>              <span class="mi">15</span>              <span class="mi">24</span>              <span class="mi">17</span>              <span class="mi">21</span>
 <span class="mi">1</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">GACC</span>             <span class="mi">20</span>              <span class="mi">18</span>               <span class="mi">3</span>              <span class="mi">26</span>               <span class="mi">4</span>
 <span class="mi">2</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">ATCG</span>              <span class="mi">2</span>               <span class="mi">1</span>               <span class="mi">5</span>              <span class="mi">16</span>               <span class="mi">0</span>
 <span class="mi">3</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">CCGA</span>             <span class="mi">14</span>              <span class="mi">29</span>              <span class="mi">23</span>               <span class="mi">2</span>              <span class="mi">19</span>
</pre></div>
</div>
<div class="admonition note">
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<p class="admonition-title">Note</p>
<p>Input files are automatically dectected from the input directory based on their extensions. Supported extensions are <strong>.fa</strong>, <strong>.fa.gz</strong>, <strong>.fq</strong>, <strong>.fq.gz</strong>, <strong>.fasta</strong>, <strong>.fasta.gz</strong>, <strong>.fastq</strong>, <strong>.fastq.gz</strong>, <strong>.fna</strong>, and <strong>.fna.gz</strong>. Individual IDs in the output table will be inferred from the input files names after removing the extension. For instance, a file named <strong>individual_1.fastq.gz</strong> will be attributed the ID <strong>individual_1</strong>. Make sure to use the same IDs when creating the population map.</p>
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</div>
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<hr class="docutils" />
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</div>
<div class="section" id="distrib">
<span id="distrib-usage"></span><h2>distrib<a class="headerlink" href="#distrib" title="Permalink to this headline"></a></h2>
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<p>Generate a table containing the distribution of markers between two groups of individuals defined in a <a class="reference internal" href="input_files.html#population-map"><span class="std std-ref">Population map</span></a>.</p>
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<p><strong>Command</strong></p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">radsex</span> <span class="n">distrib</span> <span class="o">--</span><span class="n">markers</span><span class="o">-</span><span class="n">table</span> <span class="n">markers_table_path</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">file</span> <span class="n">output_file_path</span> <span class="o">--</span><span class="n">popmap</span> <span class="n">popmap_path</span> <span class="p">[</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">depth</span> <span class="n">min_depth</span> <span class="o">--</span><span class="n">groups</span> <span class="n">group1</span><span class="p">,</span><span class="n">group2</span> <span class="o">--</span><span class="n">signif</span><span class="o">-</span><span class="n">threshold</span> <span class="n">signif_threshold</span> <span class="o">--</span><span class="n">disable</span><span class="o">-</span><span class="n">correction</span> <span class="p">]</span>
</pre></div>
</div>
<p><strong>Options</strong></p>
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<table class="docutils align-default">
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<colgroup>
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<col style="width: 20%" />
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<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
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</tr>
</thead>
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<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--markers-table,</span> <span class="pre">-t</span></code></p></td>
<td><p>Path to a marker depths table generated by “process”</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--popmap,</span> <span class="pre">-p</span></code></p></td>
<td><p>Path to a tabulated file specifying groups for all individuals</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the output file (distribution of markers between groups)</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></p></td>
<td><p>Minimum depth to consider a marker present in an individual</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--groups,</span> <span class="pre">-G</span></code></p></td>
<td><p>Names of the groups to compare if there are more than two groups in the popmap (–groups group1, group2)</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--signif-threshold,</span> <span class="pre">-S</span></code></p></td>
<td><p>P-value threshold to consider a marker significantly associated with a phenotypic group</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--disable-correction,</span> <span class="pre">-C</span></code></p></td>
<td><p>If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group</p></td>
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<p><strong>Output</strong></p>
<p>A <a class="reference internal" href="output_files.html#sex-distribution-file"><span class="std std-ref">Distribution of markers between groups</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Males</span>    <span class="n">Females</span>    <span class="n">Markers</span>       <span class="n">P</span>     <span class="n">Signif</span>      <span class="n">Bias</span>
    <span class="mi">0</span>          <span class="mi">1</span>          <span class="mi">7</span>       <span class="mi">1</span>     <span class="kc">False</span>     <span class="o">-</span><span class="mf">0.333</span>
    <span class="mi">0</span>          <span class="mi">2</span>          <span class="mi">3</span>    <span class="mf">0.39</span>     <span class="kc">False</span>     <span class="o">-</span><span class="mf">0.666</span>
    <span class="mi">0</span>          <span class="mi">3</span>          <span class="mi">1</span>    <span class="mf">0.10</span>     <span class="kc">False</span>     <span class="o">-</span><span class="mf">1.000</span>
    <span class="mi">1</span>          <span class="mi">0</span>          <span class="mi">6</span>       <span class="mi">1</span>     <span class="kc">False</span>      <span class="mf">0.333</span>
    <span class="mi">1</span>          <span class="mi">1</span>          <span class="mi">5</span>       <span class="mi">1</span>     <span class="kc">False</span>      <span class="mf">0.000</span>
    <span class="mi">1</span>          <span class="mi">2</span>          <span class="mi">1</span>       <span class="mi">1</span>     <span class="kc">False</span>     <span class="o">-</span><span class="mf">0.333</span>
    <span class="mi">1</span>          <span class="mi">3</span>          <span class="mi">2</span>    <span class="mf">0.39</span>     <span class="kc">False</span>     <span class="o">-</span><span class="mf">0.666</span>
    <span class="mi">2</span>          <span class="mi">0</span>          <span class="mi">3</span>    <span class="mf">0.39</span>     <span class="kc">False</span>      <span class="mf">0.666</span>
    <span class="mi">2</span>          <span class="mi">1</span>          <span class="mi">8</span>       <span class="mi">1</span>     <span class="kc">False</span>      <span class="mf">0.333</span>
    <span class="mi">2</span>          <span class="mi">2</span>          <span class="mi">4</span>       <span class="mi">1</span>     <span class="kc">False</span>      <span class="mf">0.000</span>
    <span class="mi">2</span>          <span class="mi">3</span>          <span class="mi">2</span>       <span class="mi">1</span>     <span class="kc">False</span>     <span class="o">-</span><span class="mf">0.333</span>
    <span class="mi">3</span>          <span class="mi">0</span>          <span class="mi">4</span>    <span class="mf">0.10</span>     <span class="kc">False</span>      <span class="mf">1.000</span>
    <span class="mi">3</span>          <span class="mi">1</span>          <span class="mi">7</span>    <span class="mf">0.39</span>     <span class="kc">False</span>      <span class="mf">0.666</span>
    <span class="mi">3</span>          <span class="mi">2</span>          <span class="mi">6</span>       <span class="mi">1</span>     <span class="kc">False</span>      <span class="mf">0.333</span>
    <span class="mi">3</span>          <span class="mi">3</span>          <span class="mi">9</span>       <span class="mi">1</span>     <span class="kc">False</span>      <span class="mf">0.000</span>
</pre></div>
</div>
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<div class="section" id="signif">
<span id="signif-usage"></span><h2>signif<a class="headerlink" href="#signif" title="Permalink to this headline"></a></h2>
<p>Find markers significantly associated with groups of individuals defined in a <a class="reference internal" href="input_files.html#population-map"><span class="std std-ref">Population map</span></a>.</p>
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<p><strong>Command</strong></p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">radsex</span> <span class="n">signif</span> <span class="o">--</span><span class="n">markers</span><span class="o">-</span><span class="n">table</span> <span class="n">markers_table_path</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">file</span> <span class="n">output_file_path</span> <span class="o">--</span><span class="n">popmap</span> <span class="n">popmap_path</span> <span class="p">[</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">depth</span> <span class="n">min_depth</span> <span class="o">--</span><span class="n">groups</span> <span class="n">group1</span><span class="p">,</span><span class="n">group2</span> <span class="o">--</span><span class="n">signif</span><span class="o">-</span><span class="n">threshold</span> <span class="n">signif_threshold</span> <span class="o">--</span><span class="n">disable</span><span class="o">-</span><span class="n">correction</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">fasta</span> <span class="p">]</span>
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<p><strong>Options</strong></p>
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<colgroup>
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<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
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</thead>
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<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--markers-table,</span> <span class="pre">-t</span></code></p></td>
<td><p>Path to a marker depths table generated by “process”</p></td>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--popmap,</span> <span class="pre">-p</span></code></p></td>
<td><p>Path to a tabulated file specifying groups for all individuals</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the output file (distribution of markers between groups)</p></td>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></p></td>
<td><p>Minimum depth to consider a marker present in an individual</p></td>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--groups,</span> <span class="pre">-G</span></code></p></td>
<td><p>Names of the groups to compare if there are more than two groups in the popmap (–groups group1, group2)</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--signif-threshold,</span> <span class="pre">-S</span></code></p></td>
<td><p>P-value threshold to consider a marker significantly associated with a phenotypic group</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--disable-correction,</span> <span class="pre">-C</span></code></p></td>
<td><p>If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--output-fasta,</span> <span class="pre">-a</span></code></p></td>
<td><p>If set, markers are saved to a fasta file instead of a markers depth table</p></td>
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<p><strong>Output</strong></p>
<p><a class="reference internal" href="output_files.html#markers-depths-table-file"><span class="std std-ref">Markers depth table</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">#Number of markers : 4</span>
<span class="nb">id</span>   <span class="n">sequence</span>     <span class="n">individual_1</span>    <span class="n">individual_2</span>    <span class="n">individual_3</span>    <span class="n">individual_4</span>    <span class="n">individual_5</span>
 <span class="mi">0</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">TATT</span>              <span class="mi">0</span>              <span class="mi">15</span>              <span class="mi">24</span>              <span class="mi">17</span>              <span class="mi">21</span>
 <span class="mi">1</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">GACC</span>             <span class="mi">20</span>              <span class="mi">18</span>               <span class="mi">3</span>              <span class="mi">26</span>               <span class="mi">4</span>
 <span class="mi">2</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">ATCG</span>              <span class="mi">2</span>               <span class="mi">1</span>               <span class="mi">5</span>              <span class="mi">16</span>               <span class="mi">0</span>
 <span class="mi">3</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">CCGA</span>             <span class="mi">14</span>              <span class="mi">29</span>              <span class="mi">23</span>               <span class="mi">2</span>              <span class="mi">19</span>
</pre></div>
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<p><a class="reference internal" href="output_files.html#fasta-file"><span class="std std-ref">Fasta file</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">&gt;</span><span class="mi">4495827</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">21</span><span class="n">_p</span><span class="p">:</span><span class="mf">1.14577e-07</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">GGATGTGTATCCATA</span>
<span class="o">&gt;</span><span class="mi">4609394</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">23</span><span class="n">_p</span><span class="p">:</span><span class="mf">1.08057e-08</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">GGTTCCATCCCAAAT</span>
<span class="o">&gt;</span><span class="mi">4661391</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">26</span><span class="n">_p</span><span class="p">:</span><span class="mf">1.92225e-10</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">GTAGAGTGACCAGTT</span>
<span class="o">&gt;</span><span class="mi">5182569</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">22</span><span class="n">_p</span><span class="p">:</span><span class="mf">3.62243e-08</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">ACATGCTGTAAATGC</span>
<span class="o">&gt;</span><span class="mi">5625957</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">25</span><span class="n">_p</span><span class="p">:</span><span class="mf">7.91633e-10</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">CTGGAGAAGAGTAGG</span>
</pre></div>
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<div class="section" id="map">
<span id="map-usage"></span><h2>map<a class="headerlink" href="#map" title="Permalink to this headline"></a></h2>
<p>Align markers to a genome and compute bias and probability of association with group for each aligned marker.</p>
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<p><strong>Command</strong></p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">radsex</span> <span class="nb">map</span> <span class="o">--</span><span class="nb">input</span><span class="o">-</span><span class="n">file</span> <span class="n">input_file_path</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">file</span> <span class="n">output_file_path</span> <span class="o">--</span><span class="n">population</span><span class="o">-</span><span class="nb">map</span> <span class="n">popmap_file_path</span> <span class="o">--</span><span class="n">genome</span><span class="o">-</span><span class="n">file</span> <span class="n">genome_file_path</span> <span class="p">[</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">depth</span> <span class="n">min_depth</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">quality</span> <span class="n">min_quality</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">frequency</span> <span class="n">min_frequency</span> <span class="p">]</span>
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</pre></div>
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<p><strong>Options</strong></p>
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<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--markers-table,</span> <span class="pre">-t</span></code></p></td>
<td><p>Path to a marker depths table generated by “process”</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--popmap,</span> <span class="pre">-p</span></code></p></td>
<td><p>Path to a tabulated file specifying groups for all individuals</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the output file (distribution of markers between groups)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--genome-file,</span> <span class="pre">-g</span></code></p></td>
<td><p>Path to the genome file</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></p></td>
<td><p>Minimum depth to consider a marker present in an individual</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--groups,</span> <span class="pre">-G</span></code></p></td>
<td><p>Names of the groups to compare if there are more than two groups in the popmap (–groups group1, group2)</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--min-quality,</span> <span class="pre">-q</span></code></p></td>
<td><p>Minimum mapping quality to retain a marker</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--min-frequency,</span> <span class="pre">-Q</span></code></p></td>
<td><p>Minimum frequency of individuals in which a marker is present to retain a marker</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--signif-threshold,</span> <span class="pre">-S</span></code></p></td>
<td><p>P-value threshold to consider a marker significantly associated with a phenotypic group</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--disable-correction,</span> <span class="pre">-C</span></code></p></td>
<td><p>If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group</p></td>
</tr>
</tbody>
</table>
<p><strong>Output</strong></p>
<p>A <a class="reference internal" href="output_files.html#mapping-results-file"><span class="std std-ref">Alignment results</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Contig</span>    <span class="n">Position</span>       <span class="n">Length</span>     <span class="n">Marker_id</span>       <span class="n">Bias</span>             <span class="n">P</span>      <span class="n">Signif</span>
<span class="n">LG03</span>      <span class="mi">18366992</span>     <span class="mi">36623554</span>       <span class="mi">4335174</span>     <span class="o">-</span><span class="mf">0.202</span>         <span class="mf">0.073</span>      <span class="kc">False</span>
<span class="n">LG05</span>      <span class="mi">28289991</span>     <span class="mi">33792114</span>       <span class="mi">4335919</span>          <span class="mi">0</span>             <span class="mi">1</span>      <span class="kc">False</span>
<span class="n">LG05</span>      <span class="mi">29738230</span>     <span class="mi">33792114</span>       <span class="mi">4336169</span>      <span class="mf">0.149</span>         <span class="mf">0.356</span>      <span class="kc">False</span>
<span class="n">LG22</span>         <span class="mi">71119</span>     <span class="mi">28810691</span>       <span class="mi">4336631</span>      <span class="mf">0.159</span>         <span class="mf">0.162</span>      <span class="kc">False</span>
<span class="n">LG15</span>      <span class="mi">20142338</span>     <span class="mi">30000224</span>       <span class="mi">4336732</span>          <span class="mi">0</span>             <span class="mi">1</span>      <span class="kc">False</span>
<span class="n">LG02</span>      <span class="mi">26668964</span>     <span class="mi">31118443</span>       <span class="mi">4337320</span>          <span class="mi">0</span>             <span class="mi">1</span>      <span class="kc">False</span>
<span class="n">LG03</span>       <span class="mi">4463700</span>     <span class="mi">36623554</span>       <span class="mi">4337383</span>     <span class="o">-</span><span class="mf">0.033</span>         <span class="mf">0.973</span>      <span class="kc">False</span>
<span class="n">LG13</span>      <span class="mi">32240045</span>     <span class="mi">33409148</span>       <span class="mi">4338936</span>     <span class="o">-</span><span class="mf">0.073</span>         <span class="mf">0.704</span>      <span class="kc">False</span>
<span class="n">LG13</span>      <span class="mi">19113343</span>     <span class="mi">33409148</span>       <span class="mi">4340342</span>      <span class="mf">0.064</span>         <span class="mf">0.479</span>      <span class="kc">False</span>
<span class="n">LG22</span>      <span class="mi">22503191</span>     <span class="mi">28810691</span>       <span class="mi">4341087</span>     <span class="o">-</span><span class="mf">0.080</span>         <span class="mf">0.704</span>      <span class="kc">False</span>
<span class="n">LG01</span>      <span class="mi">17881236</span>     <span class="mi">39973033</span>       <span class="mi">8678129</span>     <span class="o">-</span><span class="mf">0.736</span>     <span class="mf">3.417e-08</span>      <span class="kc">True</span>
<span class="n">LG01</span>      <span class="mi">16475480</span>     <span class="mi">39973033</span>       <span class="mi">8888270</span>     <span class="o">-</span><span class="mf">0.705</span>     <span class="mf">1.462e-07</span>      <span class="kc">True</span>
<span class="n">LG01</span>      <span class="mi">15761951</span>     <span class="mi">39973033</span>       <span class="mi">8954765</span>     <span class="o">-</span><span class="mf">0.769</span>     <span class="mf">8.054e-09</span>      <span class="kc">True</span>
<span class="n">LG01</span>      <span class="mi">16562550</span>     <span class="mi">39973033</span>       <span class="mi">8990122</span>     <span class="o">-</span><span class="mf">0.736</span>     <span class="mf">3.417e-08</span>      <span class="kc">True</span>
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</pre></div>
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<div class="section" id="subset">
<span id="subset-usage"></span><h2>subset<a class="headerlink" href="#subset" title="Permalink to this headline"></a></h2>
<p>Extract a subset of markers from a markers depth table based on presence in individuals from each compared group.</p>
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<p><strong>Command</strong></p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">radsex</span> <span class="n">distrib</span> <span class="o">--</span><span class="n">markers</span><span class="o">-</span><span class="n">table</span> <span class="n">markers_table_path</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">file</span> <span class="n">output_file_path</span> <span class="o">--</span><span class="n">popmap</span> <span class="n">popmap_path</span> <span class="p">[</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">depth</span> <span class="n">min_depth</span> <span class="o">--</span><span class="n">groups</span> <span class="n">group1</span><span class="p">,</span><span class="n">group2</span> <span class="o">--</span><span class="n">signif</span><span class="o">-</span><span class="n">threshold</span> <span class="n">signif_threshold</span> <span class="o">--</span><span class="n">disable</span><span class="o">-</span><span class="n">correction</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">group1</span> <span class="n">min_group1</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">group2</span> <span class="n">min_group2</span> <span class="o">--</span><span class="nb">max</span><span class="o">-</span><span class="n">group1</span> <span class="n">max_group1</span> <span class="o">--</span><span class="nb">max</span><span class="o">-</span><span class="n">group2</span> <span class="n">max_group2</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">individuals</span> <span class="n">min_individuals</span> <span class="o">--</span><span class="nb">max</span><span class="o">-</span><span class="n">individuals</span> <span class="n">max_individuals</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">fasta</span> <span class="p">]</span>
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<p><strong>Options</strong></p>
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<table class="docutils align-default">
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--markers-table,</span> <span class="pre">-t</span></code></p></td>
<td><p>Path to a marker depths table generated by “process”</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--popmap,</span> <span class="pre">-p</span></code></p></td>
<td><p>Path to a tabulated file specifying groups for all individuals</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the output file (subset of markers)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></p></td>
<td><p>Minimum depth to consider a marker present in an individual</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--groups,</span> <span class="pre">-G</span></code></p></td>
<td><p>Names of the groups to compare if there are more than two groups in the popmap (–groups group1, group2)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--signif-threshold,</span> <span class="pre">-S</span></code></p></td>
<td><p>P-value threshold to consider a marker significantly associated with a phenotypic group</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--disable-correction,</span> <span class="pre">-C</span></code></p></td>
<td><p>If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--output-fasta,</span> <span class="pre">-a</span></code></p></td>
<td><p>If set, markers are saved to a fasta file instead of a markers depth table</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--min-group1,</span> <span class="pre">-m</span></code></p></td>
<td><p>Minimum number of individuals from the first group to retain a marker in the subset</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--min-group2,</span> <span class="pre">-n</span></code></p></td>
<td><p>Minimum number of individuals from the second group to retain a marker in the subset</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--max-group1,</span> <span class="pre">-M</span></code></p></td>
<td><p>Maximum number of individuals from the first group to retain a marker in the subset</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--max-group2,</span> <span class="pre">-N</span></code></p></td>
<td><p>Maximum number of individuals from the second group to retain a marker in the subset</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--min-individuals,</span> <span class="pre">-i</span></code></p></td>
<td><p>Minimum number of individuals to retain a marker in the subset</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--max-individuals,</span> <span class="pre">-I</span></code></p></td>
<td><p>Maximum number of individuals to retain a marker in the subset</p></td>
</tr>
</tbody>
</table>
<p><strong>Output</strong></p>
<p><a class="reference internal" href="output_files.html#markers-depths-table-file"><span class="std std-ref">Markers depth table</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">#Number of markers : 4</span>
<span class="nb">id</span>   <span class="n">sequence</span>     <span class="n">individual_1</span>    <span class="n">individual_2</span>    <span class="n">individual_3</span>    <span class="n">individual_4</span>    <span class="n">individual_5</span>
 <span class="mi">0</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">TATT</span>              <span class="mi">0</span>              <span class="mi">15</span>              <span class="mi">24</span>              <span class="mi">17</span>              <span class="mi">21</span>
 <span class="mi">1</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">GACC</span>             <span class="mi">20</span>              <span class="mi">18</span>               <span class="mi">3</span>              <span class="mi">26</span>               <span class="mi">4</span>
 <span class="mi">2</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">ATCG</span>              <span class="mi">2</span>               <span class="mi">1</span>               <span class="mi">5</span>              <span class="mi">16</span>               <span class="mi">0</span>
 <span class="mi">3</span>   <span class="n">TGCA</span><span class="o">..</span><span class="n">CCGA</span>             <span class="mi">14</span>              <span class="mi">29</span>              <span class="mi">23</span>               <span class="mi">2</span>              <span class="mi">19</span>
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<p><a class="reference internal" href="output_files.html#fasta-file"><span class="std std-ref">Fasta file</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">&gt;</span><span class="mi">4495827</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">21</span><span class="n">_p</span><span class="p">:</span><span class="mf">1.14577e-07</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">GGATGTGTATCCATA</span>
<span class="o">&gt;</span><span class="mi">4609394</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">23</span><span class="n">_p</span><span class="p">:</span><span class="mf">1.08057e-08</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">GGTTCCATCCCAAAT</span>
<span class="o">&gt;</span><span class="mi">4661391</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">26</span><span class="n">_p</span><span class="p">:</span><span class="mf">1.92225e-10</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">GTAGAGTGACCAGTT</span>
<span class="o">&gt;</span><span class="mi">5182569</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">22</span><span class="n">_p</span><span class="p">:</span><span class="mf">3.62243e-08</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">ACATGCTGTAAATGC</span>
<span class="o">&gt;</span><span class="mi">5625957</span><span class="n">_F</span><span class="p">:</span><span class="mi">0</span><span class="n">_M</span><span class="p">:</span><span class="mi">25</span><span class="n">_p</span><span class="p">:</span><span class="mf">7.91633e-10</span><span class="n">_mindepth</span><span class="p">:</span><span class="mi">10</span>
<span class="n">TGCAG</span><span class="o">.....</span><span class="n">CTGGAGAAGAGTAGG</span>
</pre></div>
</div>
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</div>
<div class="section" id="freq">
<span id="freq-usage"></span><h2>freq<a class="headerlink" href="#freq" title="Permalink to this headline"></a></h2>
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<p>Generate a table containing the distribution of markers in the entire dataset.</p>
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<p><strong>Command</strong></p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">radsex</span> <span class="n">freq</span> <span class="o">--</span><span class="n">markers</span><span class="o">-</span><span class="n">table</span> <span class="n">markers_table_path</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">file</span> <span class="n">output_file_path</span> <span class="p">[</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">depth</span> <span class="n">min_depth</span> <span class="p">]</span>
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<p><strong>Options</strong></p>
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<table class="docutils align-default">
<colgroup>
<col style="width: 30%" />
<col style="width: 70%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--markers-table,</span> <span class="pre">-t</span></code></p></td>
<td><p>Path to a marker depths table generated by “process”</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the output file (distribution of markers between groups)</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></p></td>
<td><p>Minimum depth to consider a marker present in an individual</p></td>
</tr>
</tbody>
</table>
<p><strong>Output</strong></p>
<p>A <a class="reference internal" href="output_files.html#freq-results-file"><span class="std std-ref">Distribution of markers in the population</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Frequency</span>     <span class="n">Count</span>
        <span class="mi">1</span>     <span class="mi">10389</span>
        <span class="mi">2</span>      <span class="mi">3869</span>
        <span class="mi">3</span>      <span class="mi">2884</span>
        <span class="mi">4</span>      <span class="mi">1824</span>
        <span class="mi">5</span>      <span class="mi">1672</span>
        <span class="mi">6</span>      <span class="mi">1276</span>
        <span class="mi">7</span>      <span class="mi">1261</span>
        <span class="mi">8</span>      <span class="mi">1278</span>
        <span class="mi">9</span>      <span class="mi">1355</span>
        <span class="mi">10</span>     <span class="mi">1291</span>
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<div class="section" id="depth">
<span id="depth-usage"></span><h2>depth<a class="headerlink" href="#depth" title="Permalink to this headline"></a></h2>
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<p>Compute the minimum, maximum, median, and average marker depth in each individual from the dataset.</p>
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<p><strong>Command</strong></p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">radsex</span> <span class="n">depth</span> <span class="o">--</span><span class="n">markers</span><span class="o">-</span><span class="n">table</span> <span class="n">markers_table_path</span> <span class="o">--</span><span class="n">popmap</span> <span class="n">popmap_file</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">file</span> <span class="n">output_file_path</span>
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<p><strong>Options</strong></p>
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<table class="docutils align-default">
<colgroup>
<col style="width: 30%" />
<col style="width: 70%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--markers-table,</span> <span class="pre">-t</span></code></p></td>
<td><p>Path to a marker depths table generated by “process”</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--popmap,</span> <span class="pre">-p</span></code></p></td>
<td><p>Path to a tabulated file specifying groups for all individuals</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the output file (distribution of markers between groups)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></p></td>
<td><p>Minimum depth to consider a marker present in an individual</p></td>
</tr>
</tbody>
</table>
<p><strong>Output</strong></p>
<p>A <a class="reference internal" href="output_files.html#depth-results-file"><span class="std std-ref">Distribution of marker depth in each individual</span></a>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Individual</span>    <span class="n">Group</span>    <span class="n">Markers</span>    <span class="n">Retained</span>    <span class="n">Min_depth</span>    <span class="n">Max_depth</span>    <span class="n">Median_depth</span>    <span class="n">Average_depth</span>
<span class="n">SRR1519834</span>    <span class="n">M</span>        <span class="mi">1084439</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">60604</span>              <span class="mi">60</span>               <span class="mi">71</span>
<span class="n">SRR1519837</span>    <span class="n">M</span>         <span class="mi">914664</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">48628</span>              <span class="mi">44</span>               <span class="mi">53</span>
<span class="n">SRR1519830</span>    <span class="n">F</span>        <span class="mi">1165312</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">35358</span>              <span class="mi">54</span>               <span class="mi">72</span>
<span class="n">SRR1519853</span>    <span class="n">M</span>         <span class="mi">500353</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">27276</span>              <span class="mi">28</span>               <span class="mi">33</span>
<span class="n">SRR1519824</span>    <span class="n">F</span>         <span class="mi">498666</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">23912</span>              <span class="mi">21</span>               <span class="mi">27</span>
<span class="n">SRR1519819</span>    <span class="n">F</span>         <span class="mi">552423</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">36001</span>              <span class="mi">24</span>               <span class="mi">32</span>
<span class="n">SRR1519846</span>    <span class="n">M</span>         <span class="mi">522372</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">30307</span>              <span class="mi">31</span>               <span class="mi">36</span>
<span class="n">SRR1519829</span>    <span class="n">F</span>         <span class="mi">944099</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">64723</span>              <span class="mi">45</span>               <span class="mi">61</span>
<span class="n">SRR1519812</span>    <span class="n">F</span>         <span class="mi">781177</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">44358</span>              <span class="mi">36</span>               <span class="mi">46</span>
<span class="n">SRR1519862</span>    <span class="n">M</span>        <span class="mi">1313850</span>       <span class="mi">72938</span>            <span class="mi">0</span>        <span class="mi">64356</span>              <span class="mi">69</span>               <span class="mi">81</span>
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