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699 </a>
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700 <span itemprop="dateModified"><relative-time datetime="2018-06-28T09:30:36Z">Jun 28, 2018</relative-time></span>
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701 </div>
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702 </div>
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705
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706 <div class="file-wrap">
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708 <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/0816edd870fef962e6ab76a7d831917a6ef6a6c3">Permalink</a>
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709
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710 <table class="files js-navigation-container js-active-navigation-container" data-pjax>
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713 <tbody>
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715 <td class="icon"><svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg></td>
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716 <td class="content" colspan="3">Failed to load latest commit information.</td>
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723 </td>
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725 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="MuSE-wrappers" id="6eeb64d3373c86de0d266d51ca7aad6d-5ad7ff1d5254207913649df43ac24dc94ce9beeb" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/MuSE-wrappers">MuSE-wrappers</a></span>
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726 </td>
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727 <td class="message">
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728 <span class="css-truncate css-truncate-target">
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729 <a data-pjax="true" title="renamed" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/db217a791b5adeaaa396e6410f590f1dd083f56b">renamed</a>
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730 </span>
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731 </td>
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732 <td class="age">
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733 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-27T09:27:20Z">Jun 27, 2018</time-ago></span>
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734 </td>
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737 <td class="icon">
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738 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
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739 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
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740 </td>
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742 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="Mutect2-wrapper" id="7298d96c43b1f2394bd6e17cfdc622b3-1a6e9b10f4bd715c4d31f566f5c8c71f23c20915" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/Mutect2-wrapper">Mutect2-wrapper</a></span>
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743 </td>
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744 <td class="message">
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745 <span class="css-truncate css-truncate-target">
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746 <a data-pjax="true" title="order_change" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/0816edd870fef962e6ab76a7d831917a6ef6a6c3">order_change</a>
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747 </span>
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748 </td>
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749 <td class="age">
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750 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-28T09:30:36Z">Jun 28, 2018</time-ago></span>
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751 </td>
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752 </tr>
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753 <tr class="js-navigation-item">
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754 <td class="icon">
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755 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
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756 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
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757 </td>
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758 <td class="content">
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759 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="fpfilter-wrapper" id="b8e9ac11418f2ca943696e2ae7ade2c1-03fccac761b2e73a7c7aa57e407595df6d73c94f" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/fpfilter-wrapper">fpfilter-wrapper</a></span>
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760 </td>
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761 <td class="message">
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762 <span class="css-truncate css-truncate-target">
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763 <a data-pjax="true" title="test-data" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/cb43d2cf8d3a96e3538290dbbcabd35eb0241ae2">test-data</a>
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764 </span>
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765 </td>
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766 <td class="age">
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767 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-05-11T09:58:45Z">May 11, 2018</time-ago></span>
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768 </td>
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769 </tr>
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770 <tr class="js-navigation-item">
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771 <td class="icon">
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772 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
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773 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
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774 </td>
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775 <td class="content">
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776 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="somatic-sniper-wrapper" id="fb1b18b4869b8add123840bcbf1c8ec4-47b039289242e13ff648b40e41af303faaca601f" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/somatic-sniper-wrapper">somatic-sniper-wrapper</a></span>
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777 </td>
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778 <td class="message">
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779 <span class="css-truncate css-truncate-target">
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780 <a data-pjax="true" title="test_part" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/8b532e1bd87b7cf17059e325a60ed6cef0ea05df">test_part</a>
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781 </span>
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782 </td>
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783 <td class="age">
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784 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-22T13:15:39Z">Jun 22, 2018</time-ago></span>
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785 </td>
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786 </tr>
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787 <tr class="js-navigation-item">
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789 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
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790 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
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791 </td>
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792 <td class="content">
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793 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="vep86_vcf2maf-wrapper" id="e38ee16d2b256818c33d0541312f040c-78cb195337d66a39abb4661691074ba92f4425b9" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/vep86_vcf2maf-wrapper">vep86_vcf2maf-wrapper</a></span>
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794 </td>
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795 <td class="message">
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796 <span class="css-truncate css-truncate-target">
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797 <a data-pjax="true" title="renamed" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/db217a791b5adeaaa396e6410f590f1dd083f56b">renamed</a>
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798 </span>
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799 </td>
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800 <td class="age">
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801 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-27T09:27:20Z">Jun 27, 2018</time-ago></span>
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802 </td>
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803 </tr>
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804 <tr class="js-navigation-item">
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805 <td class="icon">
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806 <svg class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
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807 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
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808 </td>
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809 <td class="content">
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810 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="LICENSE" id="9879d6db96fd29134fc802214163b95a-4eb8dbddf70d795e05ea7b0e726ad57a2518ac6d" itemprop="license" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/LICENSE">LICENSE</a></span>
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811 </td>
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812 <td class="message">
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813 <span class="css-truncate css-truncate-target">
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814 <a data-pjax="true" title="Initial commit" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/7113c7c00c0852eae67102e479346822ef3c2c81">Initial commit</a>
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815 </span>
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816 </td>
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817 <td class="age">
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818 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-04-09T08:25:03Z">Apr 9, 2018</time-ago></span>
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819 </td>
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820 </tr>
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821 <tr class="js-navigation-item">
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822 <td class="icon">
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823 <svg class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
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824 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
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825 </td>
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826 <td class="content">
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827 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="README.md" id="04c6e90faac2675aa89e2176d2eec7d8-d5bc11a7b913ef494c676b275fae35a4760c6956" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/README.md">README.md</a></span>
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828 </td>
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829 <td class="message">
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830 <span class="css-truncate css-truncate-target">
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831 <a data-pjax="true" title="update" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/6ec4b8217c8c8ae7e98e3038190524b82617a3e6">update</a>
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832 </span>
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833 </td>
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834 <td class="age">
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835 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-27T13:37:21Z">Jun 27, 2018</time-ago></span>
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836 </td>
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837 </tr>
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838 <tr class="js-navigation-item">
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839 <td class="icon">
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840 <svg class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
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841 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
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842 </td>
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843 <td class="content">
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844 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="shed_tool_add.xml" id="35140ba3b6329aea1a67251631945339-0f848762d0c898cba30bbfad90c44f9ba4ea4243" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/shed_tool_add.xml">shed_tool_add.xml</a></span>
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845 </td>
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846 <td class="message">
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847 <span class="css-truncate css-truncate-target">
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848 <a data-pjax="true" title="config_file" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/f2c7a2ea607b05d784ff44f699af85e9b06f2742">config_file</a>
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849 </span>
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850 </td>
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851 <td class="age">
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852 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-05-10T14:21:46Z">May 10, 2018</time-ago></span>
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853 </td>
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854 </tr>
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855 </tbody>
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856 </table>
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857
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858 </div>
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859
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860
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861
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862 <div id="readme" class="readme boxed-group clearfix announce instapaper_body md">
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863 <h3>
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864 <svg class="octicon octicon-book" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M3 5h4v1H3V5zm0 3h4V7H3v1zm0 2h4V9H3v1zm11-5h-4v1h4V5zm0 2h-4v1h4V7zm0 2h-4v1h4V9zm2-6v9c0 .55-.45 1-1 1H9.5l-1 1-1-1H2c-.55 0-1-.45-1-1V3c0-.55.45-1 1-1h5.5l1 1 1-1H15c.55 0 1 .45 1 1zm-8 .5L7.5 3H2v9h6V3.5zm7-.5H9.5l-.5.5V12h6V3z"/></svg>
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865 README.md
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866 </h3>
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867
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868 <article class="markdown-body entry-content" itemprop="text"><h1><a id="user-content-gdc-dna-seq-pipeline-galaxy-wrapper" class="anchor" aria-hidden="true" href="#gdc-dna-seq-pipeline-galaxy-wrapper"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>GDC-DNA-Seq-pipeline-galaxy-wrapper</h1>
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869 <p>The GDC DNA-Seq analysis pipeline identifies somatic variants within whole exome sequencing (WXS) and whole genome sequencing (WGS) data. Somatic variants are identified by comparing allele frequencies in normal and tumor sample alignments, annotating each mutation, and aggregating mutations from multiple cases into one project file.</p>
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870 <p>The first pipeline starts with a reference alignment step followed by co-cleaning to increase the alignment quality. Four different variant calling pipelines are then implemented separately to identify somatic mutations. Somatic-caller-identified variants are then annotated. An aggregation pipeline incorporates variants from all cases in one project into a MAF file for each pipeline.</p>
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871 <p>DNA-Seq analysis is implemented across six main procedures:</p>
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872 <ul>
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873 <li>Genome Alignment</li>
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874 <li>Alignment Co-Cleaning</li>
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875 <li>Somatic Variant Calling</li>
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876 <li>Variant Annotation</li>
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877 <li>Mutation Aggregation</li>
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878 </ul>
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879 <p><strong>Genome Alignment</strong></p>
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880 <p>Read groups are aligned to the reference genome BWA-MEM if mean read length is greater than or equal to 70 bp. Otherwise BWA-aln is used.
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881 Each read group is aligned to the reference genome separately and all read group alignments that belong to a single aliquot are merged using SortSam and MergeSamFiles (Picard Tools).</p>
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882 <p><strong>Co-cleaning Workflow</strong></p>
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883 <p>Co-cleaning is performed as a separate pipeline as it uses multiple BAM files (i.e. the tumor BAM and normal tissue BAM) associated with the same patient. Both steps of this process are implemented using GATK</p>
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884 <pre><code>* Local realignment of insertions and deletions is performed using IndelRealigner
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885 * A base quality score recalibration (BQSR) step is then performed using BaseRecalibrator.
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886 * A filter reads step is preformed by Printreads
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887 </code></pre>
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888 <p><strong>Somatic Variant Calling</strong></p>
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889 <p>Aligned and co-cleaned BAM files are processed through the Somatic Mutation Calling Workflow as tumor-normal pairs.
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890 Variant calling is performed using four separate pipelines:</p>
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891 <pre><code>* MuSE
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892 * MuTect2
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893 * VarScan2
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894 * SomaticSniper
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895 </code></pre>
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896 <p><strong>Variant Call Annotation Workflow</strong></p>
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897 <p>Raw VCF files are then annotated in the Somatic Annotation Workflow with the Variant Effect Predictor v84
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898 In addition to annotation False Positive Filter is used to label low quality variants in VarScan and SomaticSniper outputs.</p>
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899 <p><strong>Somatic Agregation Workflow</strong></p>
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900 <p>multiple vcf file can merged and using vcf2maf a MAF file from multiple vcf can be created.</p>
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901 <p>#More informations at
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902 <a href="https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#file-access-and-availability" rel="nofollow">https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#file-access-and-availability</a></p>
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903 <p><em>All the tools and option used in the command line pipeline can be used throught galaxy wrappers</em></p>
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904 </article>
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