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@@ -1176,7 +1176,7 @@ <h4 id="submit-a-single-file">Submit a single file<a class="headerlink" href="#s
 <p>Command:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="nv">TOKEN</span><span class="o">=</span><span class="s2">&quot;YOUR-API-TOKEN&quot;</span><span class="p">;</span>
 <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>
-<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>curl<span class="w"> </span>https://imputationserver.sph.umich.edu/api/v2/jobs/submit/minimac4<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>curl<span class="w"> </span>https://imputationserver.sph.umich.edu/api/v2/jobs/submit/imputationserver2<span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="w">  </span>-H<span class="w"> </span><span class="s2">&quot;X-Auth-Token: </span><span class="nv">$TOKEN</span><span class="s2">&quot;</span><span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="w">  </span>-F<span class="w"> </span><span class="s2">&quot;files=@/path-to/file.vcf.gz&quot;</span><span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="w">  </span>-F<span class="w"> </span><span class="s2">&quot;refpanel=1000g-phase-3-v5&quot;</span><span class="w"> </span><span class="se">\</span>
@@ -1194,7 +1194,7 @@ <h4 id="submit-multiple-files">Submit multiple files<a class="headerlink" href="
 <p>Command:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="nv">TOKEN</span><span class="o">=</span><span class="s2">&quot;YOUR-API-TOKEN&quot;</span><span class="p">;</span>
 <a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>
-<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>curl<span class="w"> </span>https://imputationserver.sph.umich.edu/api/v2/jobs/submit/minimac4<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>curl<span class="w"> </span>https://imputationserver.sph.umich.edu/api/v2/jobs/submit/imputationserver2<span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="w">  </span>-H<span class="w"> </span><span class="s2">&quot;X-Auth-Token: </span><span class="nv">$TOKEN</span><span class="s2">&quot;</span><span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a><span class="w">  </span>-F<span class="w"> </span><span class="s2">&quot;files=@/path-to/file1.vcf.gz&quot;</span><span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a><span class="w">  </span>-F<span class="w"> </span><span class="s2">&quot;files=@/path-to/file2.vcf.gz&quot;</span><span class="w"> </span><span class="se">\</span>
@@ -1213,7 +1213,7 @@ <h4 id="submit-file-from-a-https">Submit file from a HTTP(S)<a class="headerlink
 <p>Command:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="nv">TOKEN</span><span class="o">=</span><span class="s2">&quot;YOUR-API-TOKEN&quot;</span><span class="p">;</span>
 <a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>
-<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>curl<span class="w">  </span>https://imputationserver.sph.umich.edu/api/v2/jobs/submit/minimac4<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>curl<span class="w">  </span>https://imputationserver.sph.umich.edu/api/v2/jobs/submit/imputationserver2<span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="w">  </span>-H<span class="w"> </span><span class="s2">&quot;X-Auth-Token: </span><span class="nv">$TOKEN</span><span class="s2">&quot;</span><span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a><span class="w">  </span>-F<span class="w"> </span><span class="s2">&quot;files=https://imputationserver.sph.umich.edu/static/downloads/hapmap300.chr1.recode.vcf.gz&quot;</span><span class="w"> </span><span class="se">\</span>
 <a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a><span class="w">  </span>-F<span class="w"> </span><span class="s2">&quot;files-source=http&quot;</span><span class="w"> </span><span class="se">\</span>
@@ -1247,10 +1247,10 @@ <h4 id="submit-single-vcf-file">Submit single vcf file<a class="headerlink" href
 <a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a><span class="c1"># submit new job</span>
 <a id="__codelineno-6-16" name="__codelineno-6-16" href="#__codelineno-6-16"></a><span class="n">vcf</span> <span class="o">=</span> <span class="s1">&#39;/path/to/genome.vcf.gz&#39;</span><span class="p">;</span>
 <a id="__codelineno-6-17" name="__codelineno-6-17" href="#__codelineno-6-17"></a><span class="n">files</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;files&#39;</span> <span class="p">:</span> <span class="nb">open</span><span class="p">(</span><span class="n">vcf</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)}</span>
-<a id="__codelineno-6-18" name="__codelineno-6-18" href="#__codelineno-6-18"></a><span class="n">r</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">post</span><span class="p">(</span><span class="n">url</span> <span class="o">+</span> <span class="s2">&quot;/jobs/submit/minimac4&quot;</span><span class="p">,</span> <span class="n">files</span><span class="o">=</span><span class="n">files</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span> <span class="n">headers</span><span class="o">=</span><span class="n">headers</span><span class="p">)</span>
+<a id="__codelineno-6-18" name="__codelineno-6-18" href="#__codelineno-6-18"></a><span class="n">r</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">post</span><span class="p">(</span><span class="n">url</span> <span class="o">+</span> <span class="s2">&quot;/jobs/submit/imputationserver2&quot;</span><span class="p">,</span> <span class="n">files</span><span class="o">=</span><span class="n">files</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span> <span class="n">headers</span><span class="o">=</span><span class="n">headers</span><span class="p">)</span>
 <a id="__codelineno-6-19" name="__codelineno-6-19" href="#__codelineno-6-19"></a><span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">status_code</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span>
 <a id="__codelineno-6-20" name="__codelineno-6-20" href="#__codelineno-6-20"></a>  <span class="nb">print</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">json</span><span class="p">()[</span><span class="s1">&#39;message&#39;</span><span class="p">])</span>
-<a id="__codelineno-6-21" name="__codelineno-6-21" href="#__codelineno-6-21"></a>  <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;POST /jobs/submit/minimac4 </span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">status_code</span><span class="p">))</span>
+<a id="__codelineno-6-21" name="__codelineno-6-21" href="#__codelineno-6-21"></a>  <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;POST /jobs/submit/imputationserver2 </span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">status_code</span><span class="p">))</span>
 <a id="__codelineno-6-22" name="__codelineno-6-22" href="#__codelineno-6-22"></a>
 <a id="__codelineno-6-23" name="__codelineno-6-23" href="#__codelineno-6-23"></a><span class="c1"># print response and job id</span>
 <a id="__codelineno-6-24" name="__codelineno-6-24" href="#__codelineno-6-24"></a><span class="nb">print</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">json</span><span class="p">()[</span><span class="s1">&#39;message&#39;</span><span class="p">])</span>
@@ -1275,10 +1275,10 @@ <h4 id="submit-multiple-vcf-files">Submit multiple vcf files<a class="headerlink
 <a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a><span class="n">vcf</span> <span class="o">=</span> <span class="s1">&#39;/path/to/file1.vcf.gz&#39;</span><span class="p">;</span>
 <a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a><span class="n">vcf1</span> <span class="o">=</span> <span class="s1">&#39;/path/to/file2.vcf.gz&#39;</span><span class="p">;</span>
 <a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a><span class="n">files</span> <span class="o">=</span> <span class="p">[(</span><span class="s1">&#39;files&#39;</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">vcf</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)),</span> <span class="p">(</span><span class="s1">&#39;files&#39;</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">vcf1</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))]</span>
-<a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a><span class="n">r</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">post</span><span class="p">(</span><span class="n">url</span> <span class="o">+</span> <span class="s2">&quot;/jobs/submit/minimac4&quot;</span><span class="p">,</span> <span class="n">files</span><span class="o">=</span><span class="n">files</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span> <span class="n">headers</span><span class="o">=</span><span class="n">headers</span><span class="p">)</span>
+<a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a><span class="n">r</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">post</span><span class="p">(</span><span class="n">url</span> <span class="o">+</span> <span class="s2">&quot;/jobs/submit/imputationserver2&quot;</span><span class="p">,</span> <span class="n">files</span><span class="o">=</span><span class="n">files</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span> <span class="n">headers</span><span class="o">=</span><span class="n">headers</span><span class="p">)</span>
 <a id="__codelineno-7-20" name="__codelineno-7-20" href="#__codelineno-7-20"></a><span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">status_code</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span>
 <a id="__codelineno-7-21" name="__codelineno-7-21" href="#__codelineno-7-21"></a>  <span class="nb">print</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">json</span><span class="p">()[</span><span class="s1">&#39;message&#39;</span><span class="p">])</span>
-<a id="__codelineno-7-22" name="__codelineno-7-22" href="#__codelineno-7-22"></a>  <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;POST /jobs/submit/minimac4 </span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">status_code</span><span class="p">))</span>
+<a id="__codelineno-7-22" name="__codelineno-7-22" href="#__codelineno-7-22"></a>  <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;POST /jobs/submit/imputationserver2 </span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">status_code</span><span class="p">))</span>
 <a id="__codelineno-7-23" name="__codelineno-7-23" href="#__codelineno-7-23"></a>
 <a id="__codelineno-7-24" name="__codelineno-7-24" href="#__codelineno-7-24"></a><span class="c1"># print message</span>
 <a id="__codelineno-7-25" name="__codelineno-7-25" href="#__codelineno-7-25"></a><span class="nb">print</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">json</span><span class="p">()[</span><span class="s1">&#39;message&#39;</span><span class="p">])</span>