urceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="co"># contains ex.leg file and serves as output directory</span>
<span class="fu">mkdir</span> -p ~/PhenotypeSimulator/inst/extdata/genotypes/hapgen
<span class="bu">cd</span> ~/PhenotypeSimulator/inst/extdata/genotypes/hapgen

<span class="co"># contains 1000Genomes haplotype data used for sampling</span>
<span class="va">hapdir=</span>/path/to/CEU.0908.impute.files

<span class="ex">hapgen2</span> -m <span class="va">$hapdir