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          <h1>ROHan</h1>
          <p> Joint inference of Runs of Homozygosity and rates of heterozygosity </p>
          <hr>
          <span class="credits left">Project maintained by <a href="https://github.com/grenaud">grenaud</a></span>
          
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<h1 id="ROHan">ROHan</h1>

<p>ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity outside of ROHs. ROHan can work on modern and ancient samples with signs of ancient DNA damage.</p>

<p>ROHan can work for sample with depth-of-coverage 4-5X or above for modern samples and 7-8X for damaged ancient samples. It makes the following assumptions:</p>
<ul>
<li>The per-base quality scores are sufficiently representative of the error rate, this should be the case for most modern Illumina runs.</li>
<li>Inbreeding is sufficiently recent. ROHan cannot deal with very distant and continuous inbreeding.</li>
<li>For ancient samples, you have adequately quantified the rates of ancient DNA damage (see README).</li>
</ul>


<p>The README contains usage and recommendation how to prepare your BAM file.</p>



<h3 id="Downloading">Downloading</h3>

<p>Go to <a href="https://github.com/grenaud/rohan">https://github.com/grenaud/rohan</a> and either:

<ol>  
<li> Download the ZIP </li>

or

<li> Do a:
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>
  git clone --depth 1 https://github.com/grenaud/rohan.git
</code></pre></div></div>
</li>
</ol>
</p>
	
<h3 id="installing">Installing</h3>


<ol>
  <li> make sure you have "cmake", "libtool", "libpng" and "git" installed, check for it by typing " git --version" and "cmake --version".  

For Ubuntu:
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>
     sudo apt-get install git
     sudo apt-get install cmake
     sudo apt-get install libtool
     sudo apt-get install libpng-dev
</code></pre></div></div>
For MacOS, if you have Homebrew (<a href="https://brew.sh/">https://brew.sh/</a>) installed: 
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>
     brew install git
     brew install cmake
     brew install libtool
     brew install libpng
</code></pre></div></div>
</li>
<li> make sure you have gcc that supports -std=c++11, gcc version 4.7 or above. Type "gcc -v" and check the version. For both Ubuntu and MacOS, 
</li>
<li>  As the makefile uses "git clone" to download subpackages, please make sure that the computer on which you are installing ROHan has access to the internet. Once done, simply type :
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>
cd ROHan
make
</code></pre></div></div>
For MacOS, if you get the problem: fatal error: 'lzma.h' file not found, this is a problem building htslib with homebrew, please refer to the following htslib page: <a href="https://github.com/samtools/htslib/issues/493">https://github.com/samtools/htslib/issues/493</a>

</li>

<li> (optional) Either put the executable in the overall path or add the path to your $PATH environment or add an alias to be able to run "rohan" from any directory.</li>
</ol>

<h2 id="Documentation">Documentation</h2>

<p>Please refer to the README.md in the repository for usage and frequently asked questions.</p>
	
<h2 id="authors">Authors</h2>

<ul>
  <li>Gabriel Renaud - <a href="https://github.com/grenaud">grenaud</a> gabriel [dot] reno [ at sign ] gmail.com</li>
</ul>

<h2 id="license">License</h2>

<p>This project is licensed under the GPL 3.0 License - see the LICENSE file for details</p>


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