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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/plink1-9">Debian Med / plink1.9</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/-/commit/391c3a96b4532fd9432ae9693b685d0113cda012">391c3a96</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-04-21T10:59:13+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not generate manpage with help2man
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#160024acd920be5bfa0df8d4be7d7493ca9f4f1a">
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+
debian/plink1.9.1
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/plink1-9/-/commit/391c3a96b4532fd9432ae9693b685d0113cda012#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,6 @@ Uploaders: Dylan Aïssi <daissi@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> help2man,</span>
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8
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> libatlas-base-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> liblapack-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> zlib1g-dev</span>
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<li id="160024acd920be5bfa0df8d4be7d7493ca9f4f1a">
<a href="https://salsa.debian.org/med-team/plink1-9/-/commit/391c3a96b4532fd9432ae9693b685d0113cda012#160024acd920be5bfa0df8d4be7d7493ca9f4f1a"><strong>debian/plink1.9.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TH</span> <span class="n" style="color: #333;">PLINK</span> <span class="s2" style="color: #d14;">"1"</span> <span class="s2" style="color: #d14;">"March 2020"</span> <span class="s2" style="color: #d14;">"PLINK v1.90b6.16 64-bit (19 Feb 2020)"</span> <span class="s2" style="color: #d14;">"User Commands"</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">SH</span> <span class="n" style="color: #333;">NAME</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">PLINK</span> <span class="p">\-</span> <span class="n" style="color: #333;">whole</span> <span class="n" style="color: #333;">genome</span> <span class="n" style="color: #333;">SNP</span> <span class="n" style="color: #333;">analysis</span></span>
</pre>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">SH</span> <span class="n" style="color: #333;">DESCRIPTION</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">v1</span><span class="m" style="color: #099;">.90</span><span class="n" style="color: #333;">b6</span><span class="m" style="color: #099;">.16</span> <span class="m" style="color: #099;">64</span><span class="p">\-</span><span class="n" style="color: #333;">bit</span> <span class="p">(</span><span class="m" style="color: #099;">19</span> <span class="n" style="color: #333;">Feb</span> <span class="m" style="color: #099;">2020</span><span class="p">)</span> <span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">cog</span><span class="p">\-</span><span class="n" style="color: #333;">genomics</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">plink</span><span class="p">/</span><span class="m" style="color: #099;">1.9</span><span class="p">/</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">C</span><span class="p">)</span> <span class="m" style="color: #099;">2005</span><span class="p">\-</span><span class="m" style="color: #099;">2020</span> <span class="n" style="color: #333;">Shaun</span> <span class="n" style="color: #333;">Purcell</span><span class="p">,</span> <span class="n" style="color: #333;">Christopher</span> <span class="n" style="color: #333;">Chang</span> <span class="n" style="color: #333;">GNU</span> <span class="n" style="color: #333;">General</span> <span class="k" style="font-weight: 600;">Public</span> <span class="n" style="color: #333;">License</span> <span class="n" style="color: #333;">v3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">PP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">the</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">flag</span> <span class="n" style="color: #333;">definitions</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">follow</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="p">*</span> <span class="p"><</span><span class="n" style="color: #333;">angle</span> <span class="n" style="color: #333;">brackets</span><span class="p">></span> <span class="n" style="color: #333;">denote</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">required</span> <span class="n" style="color: #333;">parameter</span><span class="p">,</span> <span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">angle</span> <span class="n" style="color: #333;">brackets</span> <span class="n" style="color: #333;">describes</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">nature</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"><span class="p">*</span> <span class="p">[</span><span class="s1" style="color: #d14;">'square brackets + single\-quotes'</span><span class="p">]</span> <span class="n" style="color: #333;">denotes</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">optional</span> <span class="n" style="color: #333;">modifier</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"><span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">EXACT</span> <span class="n" style="color: #333;">text</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">quotes</span><span class="p">.</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"><span class="p">*</span> <span class="p">[{</span><span class="n" style="color: #333;">bar</span><span class="p">|</span><span class="n" style="color: #333;">separated</span><span class="p">|</span><span class="n" style="color: #333;">braced</span><span class="p">|</span><span class="n" style="color: #333;">bracketed</span><span class="p">|</span><span class="n" style="color: #333;">values</span><span class="p">}]</span> <span class="n" style="color: #333;">denotes</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">collection</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">mutually</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="mosel"><span class="n" style="color: #333;">exclusive</span> <span class="n" style="color: #333;">optional</span> <span class="n" style="color: #333;">modifiers</span> <span class="p">(</span><span class="n" style="color: #333;">again</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">exact</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span><span class="p">).</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"><span class="n" style="color: #333;">When</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"><span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">outer</span> <span class="n" style="color: #333;">square</span> <span class="n" style="color: #333;">brackets</span><span class="p">,</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">choices</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">selected</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"><span class="p">*</span> <span class="p">[</span><span class="s1" style="color: #d14;">'quoted_text='</span><span class="p"><</span><span class="n" style="color: #333;">description</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">value</span><span class="p">>]</span> <span class="n" style="color: #333;">denotes</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">optional</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">that</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"><span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">begin</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">quoted</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">followed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">no</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"><span class="n" style="color: #333;">whitespace</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">between</span><span class="p">.</span> <span class="s1" style="color: #d14;">'|'</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">here</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">indicate</span> <span class="n" style="color: #333;">mutually</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"><span class="n" style="color: #333;">exclusive</span> <span class="k" style="font-weight: 600;">options</span><span class="p">.</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"><span class="p">*</span> <span class="p">[</span><span class="n" style="color: #333;">square</span> <span class="n" style="color: #333;">brackets</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">quotes</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">braces</span><span class="p">]</span> <span class="n" style="color: #333;">denote</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">optional</span> <span class="n" style="color: #333;">parameter</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"><span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">brackets</span> <span class="n" style="color: #333;">describes</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">nature</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">An</span> <span class="n" style="color: #333;">ellipsis</span> <span class="p">(...)</span> <span class="n" style="color: #333;">indicates</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">enter</span> <span class="n" style="color: #333;">multiple</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">type</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"><span class="n" style="color: #333;">plink</span> <span class="p"><</span><span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">flag</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...></span> <span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">flag</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...]</span> <span class="p">[</span><span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">flag</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...]</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"><span class="n" style="color: #333;">plink</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">help</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">flag</span> <span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...]</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">PP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"><span class="n" style="color: #333;">Most</span> <span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">runs</span> <span class="n" style="color: #333;">require</span> <span class="n" style="color: #333;">exactly</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">main</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">fileset</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">flags</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">defining</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">form</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">location</span><span class="p">:</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">bfile</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">prefix</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="p">.</span><span class="n" style="color: #333;">bed</span> <span class="p">+</span> <span class="p">.</span><span class="n" style="color: #333;">bim</span> <span class="p">+</span> <span class="p">.</span><span class="n" style="color: #333;">fam</span> <span class="n" style="color: #333;">prefix</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="s1" style="color: #d14;">'plink'</span><span class="p">).</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">full</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">of</span> <span class="p">.</span><span class="n" style="color: #333;">bed</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">bim</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">full</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">of</span> <span class="p">.</span><span class="n" style="color: #333;">bim</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">fam</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">full</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">of</span> <span class="p">.</span><span class="n" style="color: #333;">fam</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">keep</span><span class="p">\-</span><span class="n" style="color: #333;">autoconv</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">With</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">file</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">tfile</span><span class="p">/\-\-</span><span class="n" style="color: #333;">lfile</span><span class="p">/\-\-</span><span class="n" style="color: #333;">vcf</span><span class="p">/\-\-</span><span class="n" style="color: #333;">bcf</span><span class="p">/\-\-</span><span class="n" style="color: #333;">data</span><span class="p">/\-\-</span><span class="m" style="color: #099;">23f</span><span class="n" style="color: #333;">ile</span><span class="p">,</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"><span class="n" style="color: #333;">don</span><span class="s1" style="color: #d14;">'t delete autogenerated binary fileset at end of run.</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-file\fR [prefix]</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify .ped + .map filename prefix (default '</span><span class="n" style="color: #333;">plink</span><span class="s1" style="color: #d14;">').</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ped\fR <filename> : Specify full name of .ped file.</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-map\fR <filename> : Specify full name of .map file.</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-no\-fid\fR</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel"><span class="s1" style="color: #d14;">: .fam/.ped file does not contain column 1 (family ID).</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-no\-parents\fR</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel"><span class="s1" style="color: #d14;">: .fam/.ped file does not contain columns 3\-4 (parents).</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-no\-sex\fR</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="mosel"><span class="s1" style="color: #d14;">: .fam/.ped file does not contain column 5 (sex).</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-no\-pheno\fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="mosel"><span class="s1" style="color: #d14;">: .fam/.ped file does not contain column 6 (phenotype).</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tfile\fR [prefix] : Specify .tped + .tfam filename prefix (default '</span><span class="n" style="color: #333;">plink</span><span class="s1" style="color: #d14;">').</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tped\fR <fname></span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify full name of .tped file.</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tfam\fR <fname></span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify full name of .tfam file.</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-lfile\fR [prefix] : Specify .lgen + .map + .fam (long\-format fileset) prefix.</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-lgen\fR <fname></span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify full name of .lgen file.</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-reference\fR <fn> : Specify default allele file accompanying .lgen input.</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-allele\-count\fR</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="mosel"><span class="s1" style="color: #d14;">: When used with \fB\-\-lfile\fR/\-\-lgen + \fB\-\-reference\fR, specifies</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="mosel"><span class="s1" style="color: #d14;">that the .lgen file contains reference allele counts.</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-vcf\fR <filename> : Specify full name of .vcf or .vcf.gz file.</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-bcf\fR <filename> : Specify full name of BCF2 file.</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-data\fR [prefix]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify Oxford .gen + .sample prefix (default '</span><span class="n" style="color: #333;">plink</span><span class="s1" style="color: #d14;">').</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-gen\fR <filename> : Specify full name of .gen or .gen.gz file.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-bgen\fR <f> ['</span><span class="n" style="color: #333;">snpid</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="s1" style="color: #d14;">'] : Specify full name of .bgen file.</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-sample\fR <fname> : Specify full name of .sample file.</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-23file\fR <fname> [FID] [IID] [sex] [pheno] [pat. ID] [mat. ID] :</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="mosel"><span class="s1" style="color: #d14;">Specify 23andMe input file.</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-grm\-gz\fR [prfx]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify .grm.gz + .grm.id (GCTA rel. matrix) prefix.</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-grm\-bin\fR [prfx] : Specify .grm.bin + .grm.N.bin + .grm.id (GCTA triangular</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="mosel"><span class="s1" style="color: #d14;">binary relationship matrix) filename prefix.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-dummy\fR <sample ct> <SNP ct> [missing geno freq] [missing pheno freq]</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="mosel"><span class="s1" style="color: #d14;">[{acgt | 1234 | 12}] ['</span><span class="n" style="color: #333;">scalar</span><span class="p">\-</span><span class="n" style="color: #333;">pheno</span><span class="s1" style="color: #d14;">']</span></span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="mosel"><span class="s1" style="color: #d14;">This generates a fake input dataset with the specified number of samples</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="mosel"><span class="s1" style="color: #d14;">and SNPs. By default, the missing genotype and phenotype frequencies are</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="mosel"><span class="s1" style="color: #d14;">zero, and genotypes are As and Bs (change the latter with</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">acgt</span><span class="s1" style="color: #d14;">'/'</span><span class="m" style="color: #099;">1234</span><span class="s1" style="color: #d14;">'/'</span><span class="m" style="color: #099;">12</span><span class="s1" style="color: #d14;">'). The '</span><span class="n" style="color: #333;">scalar</span><span class="p">\-</span><span class="n" style="color: #333;">pheno</span><span class="s1" style="color: #d14;">' modifier causes a normally</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="mosel"><span class="s1" style="color: #d14;">distributed scalar phenotype to be generated instead of a binary one.</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-simulate\fR <simulation parameter file> [{tags | haps}] [{acgt | 1234 | 12}]</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-simulate\-qt\fR <sim. parameter file> [{tags | haps}] [{acgt | 1234 | 12}]</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-simulate\fR generates a fake input dataset with disease\-associated SNPs,</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="mosel"><span class="s1" style="color: #d14;">while \fB\-\-simulate\-qt\fR generates a dataset with quantitative trait loci.</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="mosel"><span class="s1" style="color: #d14;">.PP</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="mosel"><span class="s1" style="color: #d14;">Output files have names of the form '</span><span class="n" style="color: #333;">plink</span><span class="p">.<</span><span class="n" style="color: #333;">extension</span><span class="p">></span><span class="s1" style="color: #d14;">' by default. You can</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="mosel"><span class="s1" style="color: #d14;">change the '</span><span class="n" style="color: #333;">plink</span><span class="s1" style="color: #d14;">' prefix with</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-out\fR <prefix></span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify prefix for output files.</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="mosel"><span class="s1" style="color: #d14;">.PP</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="mosel"><span class="s1" style="color: #d14;">Most runs also require at least one of the following commands:</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-make\-bed\fR</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="mosel"><span class="s1" style="color: #d14;">Create a new binary fileset.</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="mosel"><span class="s1" style="color: #d14;">Unlike the automatic text\-to\-binary</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="mosel"><span class="s1" style="color: #d14;">converters (which only heed chromosome filters), this supports all of</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="mosel"><span class="s1" style="color: #d14;">PLINK'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">filtering</span> <span class="n" style="color: #333;">flags</span><span class="p">.</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">just</span><span class="p">\-</span><span class="n" style="color: #333;">bim</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">just</span><span class="p">\-</span><span class="n" style="color: #333;">fam</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="mosel"><span class="n" style="color: #333;">Variants</span> <span class="k" style="font-weight: 600;">of</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">only</span> <span class="nb" style="color: #0086b3;">write</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">new</span> <span class="p">.</span><span class="n" style="color: #333;">bim</span> <span class="k" style="font-weight: 600;">or</span> <span class="p">.</span><span class="n" style="color: #333;">fam</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="mosel"><span class="n" style="color: #333;">Can</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="mosel"><span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">only</span> <span class="p">.</span><span class="n" style="color: #333;">bim</span><span class="p">/.</span><span class="n" style="color: #333;">fam</span> <span class="n" style="color: #333;">input</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="mosel"><span class="n" style="color: #333;">USE</span> <span class="n" style="color: #333;">THESE</span> <span class="n" style="color: #333;">CAUTIOUSLY</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">easy</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">desynchronize</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">binary</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="mosel"><span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">your</span> <span class="p">.</span><span class="n" style="color: #333;">bim</span><span class="p">/.</span><span class="n" style="color: #333;">fam</span> <span class="n" style="color: #333;">indexes</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">commands</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="mosel"><span class="n" style="color: #333;">improperly</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">doubt</span><span class="p">,</span> <span class="n" style="color: #333;">stick</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">format</span><span class="p">></span> <span class="p">[{</span><span class="m" style="color: #099;">01</span> <span class="p">|</span> <span class="m" style="color: #099;">12</span><span class="p">}]</span> <span class="p">[{</span><span class="n" style="color: #333;">tab</span> <span class="p">|</span> <span class="n" style="color: #333;">tabx</span> <span class="p">|</span> <span class="n" style="color: #333;">spacex</span> <span class="p">|</span> <span class="n" style="color: #333;">bgz</span> <span class="p">|</span> <span class="n" style="color: #333;">gen</span><span class="p">\-</span><span class="n" style="color: #333;">gz</span><span class="p">}]</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'include\-alt'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'omit\-nonmale\-y'</span><span class="p">]</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="mosel"><span class="n" style="color: #333;">Create</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">fileset</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">filters</span> <span class="n" style="color: #333;">applied</span><span class="p">.</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">output</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="mosel"><span class="n" style="color: #333;">formats</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">supported</span><span class="p">:</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'23'</span><span class="p">:</span> <span class="m" style="color: #099;">23</span><span class="n" style="color: #333;">andMe</span> <span class="m" style="color: #099;">4</span><span class="p">\-</span><span class="n" style="color: #333;">column</span> <span class="n" style="color: #333;">format</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="mosel"><span class="n" style="color: #333;">sample</span><span class="s1" style="color: #d14;">'s data (\fB\-\-keep\fR may be handy), and does not support multicharacter</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="mosel"><span class="s1" style="color: #d14;">allele codes.</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">A</span><span class="s1" style="color: #d14;">': Sample\-major additive (0/1/2) coding, suitable for loading from R.</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="mosel"><span class="s1" style="color: #d14;">If you need uncounted alleles to be named in the header line, add the</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="k" style="font-weight: 600;">include</span><span class="p">\-</span><span class="n" style="color: #333;">alt</span><span class="s1" style="color: #d14;">' modifier.</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">AD</span><span class="s1" style="color: #d14;">': Sample\-major additive (0/1/2) + dominant (het=1/hom=0) coding.</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="mosel"><span class="s1" style="color: #d14;">Also supports '</span><span class="k" style="font-weight: 600;">include</span><span class="p">\-</span><span class="n" style="color: #333;">alt</span><span class="s1" style="color: #d14;">'.</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">A</span><span class="p">\-</span><span class="n" style="color: #333;">transpose</span><span class="s1" style="color: #d14;">': Variant\-major 0/1/2.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">beagle</span><span class="s1" style="color: #d14;">': Unphased per\-autosome .dat and .map files, readable by early</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="mosel"><span class="s1" style="color: #d14;">BEAGLE versions.</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">beagle</span><span class="p">\-</span><span class="n" style="color: #333;">nomap</span><span class="s1" style="color: #d14;">': Single .beagle.dat file.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">bimbam</span><span class="s1" style="color: #d14;">': Regular BIMBAM format.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">bimbam</span><span class="p">\-</span><span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">chr</span><span class="s1" style="color: #d14;">': BIMBAM format, with a two\-column .pos.txt file. Does not</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="mosel"><span class="s1" style="color: #d14;">support multiple chromosomes.</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">fastphase</span><span class="s1" style="color: #d14;">': Per\-chromosome fastPHASE files, with</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
</pre>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&.chr\-<chr #>.recode.phase.inp filename extensions.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">fastphase</span><span class="p">\-</span><span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">chr</span><span class="s1" style="color: #d14;">': Single .recode.phase.inp file.</span></span>
</pre>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="mosel"><span class="s1" style="color: #d14;">Does not support</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="mosel"><span class="s1" style="color: #d14;">multiple chromosomes.</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">HV</span><span class="s1" style="color: #d14;">': Per\-chromosome Haploview files, with .chr\-<chr #>{.ped,.info}</span></span>
</pre>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
</pre>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="mosel"><span class="s1" style="color: #d14;">filename extensions.</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">HV</span><span class="p">\-</span><span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">chr</span><span class="s1" style="color: #d14;">': Single Haploview .ped + .info file pair.</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="mosel"><span class="s1" style="color: #d14;">Does not support</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="mosel"><span class="s1" style="color: #d14;">multiple chromosomes.</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">lgen</span><span class="s1" style="color: #d14;">': PLINK 1 long\-format (.lgen + .fam + .map), loadable with \fB\-\-lfile\fR.</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">lgen</span><span class="p">\-</span><span class="n" style="color: #333;">ref</span><span class="s1" style="color: #d14;">': .lgen + .fam + .map + .ref, loadable with \fB\-\-lfile\fR +</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-reference\fR.</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="k" style="font-weight: 600;">list</span><span class="s1" style="color: #d14;">': Single genotype\-based list, up to 4 lines per variant.</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="mosel"><span class="s1" style="color: #d14;">To omit</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="mosel"><span class="s1" style="color: #d14;">nonmale genotypes on the Y chromosome, add the '</span><span class="n" style="color: #333;">omit</span><span class="p">\-</span><span class="n" style="color: #333;">nonmale</span><span class="p">\-</span><span class="n" style="color: #333;">y</span><span class="s1" style="color: #d14;">' modifier.</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">rlist</span><span class="s1" style="color: #d14;">': .rlist + .fam + .map fileset, where the .rlist file is a</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="mosel"><span class="s1" style="color: #d14;">genotype\-based list which omits the most common genotype for each</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="mosel"><span class="s1" style="color: #d14;">variant. Also supports '</span><span class="n" style="color: #333;">omit</span><span class="p">\-</span><span class="n" style="color: #333;">nonmale</span><span class="p">\-</span><span class="n" style="color: #333;">y</span><span class="s1" style="color: #d14;">'.</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">oxford</span><span class="s1" style="color: #d14;">': Oxford\-format .gen + .sample.</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="mosel"><span class="s1" style="color: #d14;">With the '</span><span class="n" style="color: #333;">gen</span><span class="p">\-</span><span class="n" style="color: #333;">gz</span><span class="s1" style="color: #d14;">' modifier, the</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&.gen file is gzipped.</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">ped</span><span class="s1" style="color: #d14;">': PLINK 1 sample\-major (.ped + .map), loadable with \fB\-\-file\fR.</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">compound</span><span class="p">\-</span><span class="n" style="color: #333;">genotypes</span><span class="s1" style="color: #d14;">': Same as '</span><span class="n" style="color: #333;">ped</span><span class="s1" style="color: #d14;">', except that the space between each</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="mosel"><span class="s1" style="color: #d14;">pair of same\-variant allele codes is removed.</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">structure</span><span class="s1" style="color: #d14;">': Structure\-format.</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">transpose</span><span class="s1" style="color: #d14;">': PLINK 1 variant\-major (.tped + .tfam), loadable with</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tfile\fR.</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">vcf</span><span class="s1" style="color: #d14;">', '</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="n" style="color: #333;">fid</span><span class="s1" style="color: #d14;">', '</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="n" style="color: #333;">iid</span><span class="s1" style="color: #d14;">': VCFv4.2.</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="n" style="color: #333;">fid</span><span class="s1" style="color: #d14;">' and '</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="n" style="color: #333;">iid</span><span class="s1" style="color: #d14;">' cause</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="mosel"><span class="s1" style="color: #d14;">family IDs or within\-family IDs respectively to be used for the sample</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="mosel"><span class="s1" style="color: #d14;">IDs in the last header row, while '</span><span class="n" style="color: #333;">vcf</span><span class="s1" style="color: #d14;">' merges both IDs and puts an</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="mosel"><span class="s1" style="color: #d14;">underscore between them. If the '</span><span class="n" style="color: #333;">bgz</span><span class="s1" style="color: #d14;">' modifier is added, the VCF file is</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="mosel"><span class="s1" style="color: #d14;">block\-gzipped.</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="mosel"><span class="s1" style="color: #d14;">The A2 allele is saved as the reference and normally flagged as not based</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="mosel"><span class="s1" style="color: #d14;">on a real reference genome (INFO:PR). When it is important for reference</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="mosel"><span class="s1" style="color: #d14;">alleles to be correct, you'</span><span class="n" style="color: #333;">ll</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">want</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">include</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">a2</span><span class="p">\-</span><span class="n" style="color: #333;">allele</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">real</span><span class="p">\-</span><span class="n" style="color: #333;">ref</span><span class="p">\-</span><span class="n" style="color: #333;">alleles</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">your</span> <span class="nf" style="color: #900; font-weight: 600;">command</span><span class="p">.</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="mosel"><span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">addition</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'12'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">A1</span> <span class="p">(</span><span class="n" style="color: #333;">usually</span> <span class="n" style="color: #333;">minor</span><span class="p">)</span> <span class="n" style="color: #333;">alleles</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">coded</span> <span class="k" style="font-weight: 600;">as</span> <span class="s1" style="color: #d14;">'1'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">A2</span> <span class="n" style="color: #333;">alleles</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">coded</span> <span class="k" style="font-weight: 600;">as</span> <span class="s1" style="color: #d14;">'2'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="s1" style="color: #d14;">'01'</span> <span class="n" style="color: #333;">maps</span> <span class="n" style="color: #333;">A1</span> <span class="p">\-></span> <span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">A2</span> <span class="p">\-></span> <span class="m" style="color: #099;">1.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'tab'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">mostly</span> <span class="n" style="color: #333;">tab</span><span class="p">\-</span><span class="n" style="color: #333;">delimited</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="mosel"><span class="n" style="color: #333;">mostly</span> <span class="n" style="color: #333;">space</span><span class="p">\-</span><span class="n" style="color: #333;">delimited</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'tabx'</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'spacex'</span> <span class="n" style="color: #333;">force</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">tabs</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">all</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="mosel"><span class="n" style="color: #333;">spaces</span><span class="p">,</span> <span class="n" style="color: #333;">respectively</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">scan</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'verbose'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">alias</span><span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flipscan</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="mosel"><span class="n" style="color: #333;">LD</span><span class="p">\-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">scan</span> <span class="n" style="color: #333;">for</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">strand</span> <span class="n" style="color: #333;">inconsistency</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">a</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">loaded</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">just</span><span class="p">\-</span><span class="n" style="color: #333;">fam</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="mosel"><span class="n" style="color: #333;">automatically</span> <span class="n" style="color: #333;">generate</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">updated</span> <span class="k" style="font-weight: 600;">version</span> <span class="p">(</span><span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">filters</span> <span class="n" style="color: #333;">applied</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="mosel"><span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="k" style="font-weight: 600;">do</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">wish</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">simultaneously</span> <span class="n" style="color: #333;">generate</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">file</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="mosel"><span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">use</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">just</span> <span class="n" style="color: #333;">produce</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">pruned</span> <span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">cluster</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'omit\-unassigned'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">clusters</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">within</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">family</span><span class="p">,</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">generates</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">new</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="mosel"><span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">file</span> <span class="p">(</span><span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">filters</span> <span class="n" style="color: #333;">applied</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'omit\-unassigned'</span> <span class="n" style="color: #333;">modifier</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="mosel"><span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">unclustered</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">omitted</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">;</span> <span class="n" style="color: #333;">otherwise</span> <span class="n" style="color: #333;">their</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="mosel"><span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">is</span> <span class="s1" style="color: #d14;">'NA'</span><span class="p">.</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">table</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">sets</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">defined</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">dumps</span> <span class="s1" style="color: #d14;">'END'</span><span class="p">\-</span><span class="n" style="color: #333;">terminated</span> <span class="k" style="font-weight: 600;">set</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="mosel"><span class="n" style="color: #333;">membership</span> <span class="n" style="color: #333;">lists</span> <span class="k" style="font-weight: 600;">to</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">prefix</span><span class="p">>.</span><span class="k" style="font-weight: 600;">set</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">table</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">writes</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="mosel"><span class="n" style="color: #333;">variant</span><span class="p">\-</span><span class="n" style="color: #333;">by</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">membership</span> <span class="n" style="color: #333;">table</span> <span class="k" style="font-weight: 600;">to</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">prefix</span><span class="p">>.</span><span class="k" style="font-weight: 600;">set</span><span class="p">.</span><span class="n" style="color: #333;">table</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><.</span><span class="n" style="color: #333;">ped</span> <span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p"><.</span><span class="n" style="color: #333;">map</span> <span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">fileset</span> <span class="n" style="color: #333;">prefix</span><span class="p">></span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">bmerge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><.</span><span class="n" style="color: #333;">bed</span> <span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p"><.</span><span class="n" style="color: #333;">bim</span> <span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p"><.</span><span class="n" style="color: #333;">fam</span> <span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">bmerge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">binary</span> <span class="n" style="color: #333;">fileset</span> <span class="n" style="color: #333;">prefix</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="mosel"><span class="n" style="color: #333;">Merge</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">fileset</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">initially</span> <span class="n" style="color: #333;">loaded</span> <span class="n" style="color: #333;">fileset</span><span class="p">,</span> <span class="n" style="color: #333;">writing</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="mosel"><span class="n" style="color: #333;">result</span> <span class="k" style="font-weight: 600;">to</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">prefix</span><span class="p">>.</span><span class="n" style="color: #333;">bed</span> <span class="p">+</span> <span class="p">.</span><span class="n" style="color: #333;">bim</span> <span class="p">+</span> <span class="p">.</span><span class="n" style="color: #333;">fam</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">longer</span> <span class="n" style="color: #333;">necessary</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="mosel"><span class="n" style="color: #333;">simultaneously</span> <span class="n" style="color: #333;">specify</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\-</span><span class="k" style="font-weight: 600;">list</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="mosel"><span class="n" style="color: #333;">Merge</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">filesets</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">fileset</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="mosel"><span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">specified</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="p">*</span><span class="n" style="color: #333;">without</span><span class="p">*</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">reference</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">case</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">newly</span> <span class="n" style="color: #333;">created</span> <span class="n" style="color: #333;">fileset</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">treated</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">by</span></span>
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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="mosel"><span class="n" style="color: #333;">most</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">operations</span><span class="p">.)</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">interpreted</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">follows</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">assumed</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">prefix</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="mosel"><span class="n" style="color: #333;">binary</span> <span class="n" style="color: #333;">fileset</span><span class="p">.</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">exactly</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">assumed</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">full</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="mosel"><span class="n" style="color: #333;">filenames</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">fileset</span> <span class="p">(.</span><span class="n" style="color: #333;">ped</span> <span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="k" style="font-weight: 600;">then</span> <span class="p">.</span><span class="n" style="color: #333;">map</span><span class="p">).</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">exactly</span> <span class="n" style="color: #333;">three</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">assumed</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">full</span></span>
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<td class="diff-line-num new new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="mosel"><span class="n" style="color: #333;">filenames</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">binary</span> <span class="n" style="color: #333;">fileset</span> <span class="p">(.</span><span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">then</span> <span class="p">.</span><span class="n" style="color: #333;">bim</span><span class="p">,</span> <span class="k" style="font-weight: 600;">then</span> <span class="p">.</span><span class="n" style="color: #333;">fam</span><span class="p">).</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">snplist</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">list</span><span class="p">\-</span><span class="m" style="color: #099;">23</span><span class="p">\-</span><span class="n" style="color: #333;">indels</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">snplist</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">writes</span> <span class="n" style="color: #333;">a</span> <span class="p">.</span><span class="n" style="color: #333;">snplist</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">listing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">variants</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="mosel"><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">pass</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">filters</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">inclusion</span> <span class="n" style="color: #333;">thresholds</span> <span class="n" style="color: #333;">you</span><span class="s1" style="color: #d14;">'ve specified, while</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-list\-23\-indels\fR writes the subset with 23andMe\-style indel calls (D/I</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="mosel"><span class="s1" style="color: #d14;">allele codes).</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-list\-duplicate\-vars\fR ['</span><span class="n" style="color: #333;">require</span><span class="p">\-</span><span class="n" style="color: #333;">same</span><span class="p">\-</span><span class="n" style="color: #333;">ref</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">ids</span><span class="p">\-</span><span class="n" style="color: #333;">only</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">suppress</span><span class="p">\-</span><span class="n" style="color: #333;">first</span><span class="s1" style="color: #d14;">']</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-list\-duplicate\-vars\fR writes a .dupvar file describing all groups of</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="mosel"><span class="s1" style="color: #d14;">variants with matching positions and allele codes.</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="mosel"><span class="s1" style="color: #d14;">* By default, A1/A2 allele assignments are ignored; use '</span><span class="n" style="color: #333;">require</span><span class="p">\-</span><span class="n" style="color: #333;">same</span><span class="p">\-</span><span class="n" style="color: #333;">ref</span><span class="s1" style="color: #d14;">'</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="mosel"><span class="s1" style="color: #d14;">to override this.</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Normally, the report contains position and allele codes.</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="mosel"><span class="s1" style="color: #d14;">To remove them</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="mosel"><span class="s1" style="color: #d14;">(and produce a file directly usable with e.g. \fB\-\-extract\fR/\-\-exclude), use</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">ids</span><span class="p">\-</span><span class="n" style="color: #333;">only</span><span class="s1" style="color: #d14;">'. Note that this command will fail in '</span><span class="n" style="color: #333;">ids</span><span class="p">\-</span><span class="n" style="color: #333;">only</span><span class="s1" style="color: #d14;">' mode if any</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="mosel"><span class="s1" style="color: #d14;">of the reported IDs are not unique.</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">suppress</span><span class="p">\-</span><span class="n" style="color: #333;">first</span><span class="s1" style="color: #d14;">' causes the first variant ID in each group to be omitted</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="mosel"><span class="s1" style="color: #d14;">from the report.</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-freq\fR [{counts | case\-control}] ['</span><span class="n" style="color: #333;">gz</span><span class="s1" style="color: #d14;">']</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-freqx\fR ['</span><span class="n" style="color: #333;">gz</span><span class="s1" style="color: #d14;">']</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-freq\fR generates a basic allele frequency (or count, if the '</span><span class="n" style="color: #333;">counts</span><span class="s1" style="color: #d14;">'</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="mosel"><span class="s1" style="color: #d14;">modifier is present) report.</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="mosel"><span class="s1" style="color: #d14;">This can be combined with \fB\-\-within\fR/\-\-family</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="mosel"><span class="s1" style="color: #d14;">to produce a cluster\-stratified allele frequency/count report instead, or</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="mosel"><span class="s1" style="color: #d14;">the '</span><span class="k" style="font-weight: 600;">case</span><span class="p">\-</span><span class="n" style="color: #333;">control</span><span class="s1" style="color: #d14;">' modifier to report case and control allele frequencies</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="mosel"><span class="s1" style="color: #d14;">separately.</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-freqx\fR generates a more detailed genotype count report, designed for use</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="mosel"><span class="s1" style="color: #d14;">with \fB\-\-read\-freq\fR.</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-missing\fR ['</span><span class="n" style="color: #333;">gz</span><span class="s1" style="color: #d14;">']</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="mosel"><span class="s1" style="color: #d14;">Generate sample\- and variant\-based missing data reports.</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="mosel"><span class="s1" style="color: #d14;">If clusters are</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="mosel"><span class="s1" style="color: #d14;">defined, the variant\-based report is cluster\-stratified.</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">gz</span><span class="s1" style="color: #d14;">' causes the</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="mosel"><span class="s1" style="color: #d14;">output files to be gzipped.</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="mosel"><span class="s1" style="color: #d14;">Unlike most other commands, this doesn'</span><span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">treat</span> <span class="n" style="color: #333;">het</span><span class="p">.</span> <span class="n" style="color: #333;">haploids</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">missing</span><span class="p">.</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">test</span><span class="p">\-</span><span class="n" style="color: #333;">mishap</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="mosel"><span class="n" style="color: #333;">Check</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">association</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">calls</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">flanking</span> <span class="n" style="color: #333;">haplotypes</span><span class="p">.</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">hardy</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'midp'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'gz'</span><span class="p">]</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="mosel"><span class="n" style="color: #333;">Generate</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Hardy</span><span class="p">\-</span><span class="n" style="color: #333;">Weinberg</span> <span class="n" style="color: #333;">exact</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">NOT</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="mosel"><span class="n" style="color: #333;">simultaneously</span> <span class="n" style="color: #333;">filter</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">more</span><span class="p">;</span> <span class="n" style="color: #333;">use</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">hwe</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">that</span><span class="p">.)</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="mosel"><span class="k" style="font-weight: 600;">With</span></span>
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<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'midp'</span> <span class="n" style="color: #333;">modifier</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">applies</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">mid</span><span class="p">\-</span><span class="n" style="color: #333;">p</span> <span class="n" style="color: #333;">adjustment</span> <span class="n" style="color: #333;">described</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="mosel"><span class="n" style="color: #333;">Graffelman</span> <span class="n" style="color: #333;">J</span><span class="p">,</span> <span class="n" style="color: #333;">Moreno</span> <span class="n" style="color: #333;">V</span> <span class="p">(</span><span class="m" style="color: #099;">2013</span><span class="p">)</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">mid</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exact</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num new new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="mosel"><span class="n" style="color: #333;">Hardy</span><span class="p">\-</span><span class="n" style="color: #333;">Weinberg</span> <span class="n" style="color: #333;">Equilibrium</span><span class="p">.</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mendel</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'summaries\-only'</span><span class="p">]</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="mosel"><span class="n" style="color: #333;">Generate</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Mendel</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'summaries\-only'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="mosel"><span class="p">\&.</span><span class="n" style="color: #333;">mendel</span> <span class="n" style="color: #333;">file</span> <span class="p">(</span><span class="n" style="color: #333;">listing</span> <span class="n" style="color: #333;">every</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">error</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">skipped</span><span class="p">.</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">het</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'small\-sample'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'gz'</span><span class="p">]</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">ibc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="mosel"><span class="n" style="color: #333;">Estimate</span> <span class="n" style="color: #333;">inbreeding</span> <span class="n" style="color: #333;">coefficients</span><span class="p">.</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">het</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">reports</span> <span class="n" style="color: #333;">method</span><span class="p">\-</span><span class="k" style="font-weight: 600;">of</span><span class="p">\-</span><span class="n" style="color: #333;">moments</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="mosel"><span class="n" style="color: #333;">estimates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">ibc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">calculates</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">three</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">described</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Yang</span> <span class="n" style="color: #333;">J</span><span class="p">,</span> <span class="n" style="color: #333;">Lee</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="mosel"><span class="n" style="color: #333;">SH</span><span class="p">,</span> <span class="n" style="color: #333;">Goddard</span> <span class="n" style="color: #333;">ME</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Visscher</span> <span class="n" style="color: #333;">PM</span> <span class="p">(</span><span class="m" style="color: #099;">2011</span><span class="p">)</span> <span class="n" style="color: #333;">GCTA</span><span class="p">:</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">Tool</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">Genome</span><span class="p">\-</span><span class="n" style="color: #333;">wide</span> <span class="n" style="color: #333;">Complex</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="mosel"><span class="n" style="color: #333;">Trait</span> <span class="n" style="color: #333;">Analysis</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">That</span> <span class="n" style="color: #333;">paper</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">describes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">relationship</span> <span class="n" style="color: #333;">matrix</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="mosel"><span class="n" style="color: #333;">computation</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">reimplement</span><span class="p">.)</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">functions</span> <span class="n" style="color: #333;">require</span> <span class="n" style="color: #333;">decent</span> <span class="n" style="color: #333;">MAF</span> <span class="n" style="color: #333;">estimates</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">few</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="mosel"><span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">immediate</span> <span class="n" style="color: #333;">fileset</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">read</span><span class="p">\-</span><span class="n" style="color: #333;">freq</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">practically</span> <span class="n" style="color: #333;">mandatory</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="mosel"><span class="n" style="color: #333;">since</span> <span class="n" style="color: #333;">imputed</span> <span class="n" style="color: #333;">MAFs</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">wildly</span> <span class="n" style="color: #333;">inaccurate</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">case</span><span class="p">.</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">They</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">assume</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">marker</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">approximate</span> <span class="n" style="color: #333;">linkage</span> <span class="n" style="color: #333;">equilibrium</span><span class="p">.</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">het</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">omits</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">n</span><span class="p">/(</span><span class="n" style="color: #333;">n</span><span class="p">\-</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">multiplier</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Nei</span><span class="s1" style="color: #d14;">'s expected</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="mosel"><span class="s1" style="color: #d14;">homozygosity formula.</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="mosel"><span class="s1" style="color: #d14;">The '</span><span class="n" style="color: #333;">small</span><span class="p">\-</span><span class="n" style="color: #333;">sample</span><span class="s1" style="color: #d14;">' modifier causes it to be</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="mosel"><span class="s1" style="color: #d14;">included, while forcing \fB\-\-het\fR to use MAFs imputed from founders in the</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="mosel"><span class="s1" style="color: #d14;">immediate dataset.</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-check\-sex\fR [female max F] [male min F]</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-check\-sex\fR ycount [female max F] [male min F] [female max Y obs]</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="mosel"><span class="s1" style="color: #d14;">[male min Y obs]</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-check\-sex\fR y\-only [female max Y obs] [male min Y obs]</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-impute\-sex\fR [female max F] [male min F]</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-impute\-sex\fR ycount [female max F] [male min F] [female max Y obs]</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="mosel"><span class="s1" style="color: #d14;">[male min Y obs]</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-impute\-sex\fR y\-only [female max Y obs] [male min Y obs]</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-check\-sex\fR normally compares sex assignments in the input dataset with</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="mosel"><span class="s1" style="color: #d14;">those imputed from X chromosome inbreeding coefficients.</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Make sure that the X chromosome pseudo\-autosomal region has been split</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="mosel"><span class="s1" style="color: #d14;">off (with e.g. \fB\-\-split\-x\fR) before using this.</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="mosel"><span class="s1" style="color: #d14;">* You also need decent MAF estimates (so, with very few samples in your</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="mosel"><span class="s1" style="color: #d14;">immediate fileset, use \fB\-\-read\-freq\fR), and your marker set should be in</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="mosel"><span class="s1" style="color: #d14;">approximate linkage equilibrium.</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="mosel"><span class="s1" style="color: #d14;">* By default, F estimates smaller than 0.2 yield female calls, and values</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="mosel"><span class="s1" style="color: #d14;">larger than 0.8 yield male calls.</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="mosel"><span class="s1" style="color: #d14;">If you pass numeric parameter(s) to</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-check\-sex\fR, the first two control these thresholds.</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="mosel"><span class="s1" style="color: #d14;">There are now two modes which consider Y chromosome data.</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="mosel"><span class="s1" style="color: #d14;">* In '</span><span class="n" style="color: #333;">ycount</span><span class="s1" style="color: #d14;">' mode, gender is still imputed from the X chromosome, but</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="mosel"><span class="s1" style="color: #d14;">female calls are downgraded to ambiguous whenever more than 0 nonmissing</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="mosel"><span class="s1" style="color: #d14;">Y genotypes are present, and male calls are downgraded when fewer than 0</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="mosel"><span class="s1" style="color: #d14;">are present. (Note that these are counts, not rates.) These thresholds</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="mosel"><span class="s1" style="color: #d14;">are controllable with \fB\-\-check\-sex\fR ycount'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">optional</span> <span class="m" style="color: #099;">3</span><span class="n" style="color: #333;">rd</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4</span><span class="n" style="color: #333;">th</span> <span class="n" style="color: #333;">numeric</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="mosel"><span class="k" style="font-weight: 600;">parameters</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">In</span> <span class="s1" style="color: #d14;">'y\-only'</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">gender</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">imputed</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">nonmissing</span> <span class="n" style="color: #333;">Y</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">counts</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">male</span> <span class="n" style="color: #333;">minimum</span> <span class="n" style="color: #333;">threshold</span> <span class="n" style="color: #333;">defaults</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">zero</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">case</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">impute</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">changes</span> <span class="n" style="color: #333;">sex</span> <span class="n" style="color: #333;">assignments</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">imputed</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="mosel"><span class="n" style="color: #333;">otherwise</span> <span class="n" style="color: #333;">identical</span> <span class="k" style="font-weight: 600;">to</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">check</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="mosel"><span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">/\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">covar</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">fst</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'case\-control'</span><span class="p">]</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">alias</span><span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">Fst</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="mosel"><span class="n" style="color: #333;">Estimate</span> <span class="n" style="color: #333;">Wright</span><span class="s1" style="color: #d14;">'s Fst for each autosomal diploid variant using the method</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="mosel"><span class="s1" style="color: #d14;">introduced in Weir BS, Cockerham CC (1984) Estimating F\-statistics for the</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="mosel"><span class="s1" style="color: #d14;">analysis of population structure, given a set of subpopulations defined via</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-within\fR. Raw and weighted global means are also reported.</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="mosel"><span class="s1" style="color: #d14;">* If you'</span><span class="n" style="color: #333;">re</span> <span class="n" style="color: #333;">interested</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">global</span> <span class="n" style="color: #333;">means</span><span class="p">,</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">usually</span> <span class="n" style="color: #333;">best</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">perform</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="mosel"><span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">marker</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">approximate</span> <span class="n" style="color: #333;">linkage</span> <span class="n" style="color: #333;">equilibrium</span><span class="p">.</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">subpopulations</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">represent</span> <span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">with</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="mosel"><span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">status</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'case\-control'</span> <span class="n" style="color: #333;">modifier</span><span class="p">.</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">indep</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">window</span> <span class="n" style="color: #333;">size</span><span class="p">>[</span><span class="s1" style="color: #d14;">'kb'</span><span class="p">]</span> <span class="p"><</span><span class="n" style="color: #333;">step</span> <span class="n" style="color: #333;">size</span> <span class="p">(</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ct</span><span class="p">)></span> <span class="p"><</span><span class="n" style="color: #333;">VIF</span> <span class="n" style="color: #333;">threshold</span><span class="p">></span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">indep</span><span class="p">\-</span><span class="n" style="color: #333;">pairwise</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">window</span> <span class="n" style="color: #333;">size</span><span class="p">>[</span><span class="s1" style="color: #d14;">'kb'</span><span class="p">]</span> <span class="p"><</span><span class="n" style="color: #333;">step</span> <span class="n" style="color: #333;">size</span> <span class="p">(</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ct</span><span class="p">)></span> <span class="p"><</span><span class="n" style="color: #333;">r</span><span class="p">^</span><span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">threshold</span><span class="p">></span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">indep</span><span class="p">\-</span><span class="n" style="color: #333;">pairphase</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">window</span> <span class="n" style="color: #333;">size</span><span class="p">>[</span><span class="s1" style="color: #d14;">'kb'</span><span class="p">]</span> <span class="p"><</span><span class="n" style="color: #333;">step</span> <span class="n" style="color: #333;">size</span> <span class="p">(</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ct</span><span class="p">)></span> <span class="p"><</span><span class="n" style="color: #333;">r</span><span class="p">^</span><span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">thresh</span><span class="p">></span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="mosel"><span class="n" style="color: #333;">Generate</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">markers</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">approximate</span> <span class="n" style="color: #333;">linkage</span> <span class="n" style="color: #333;">equilibrium</span><span class="p">.</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="mosel"><span class="k" style="font-weight: 600;">With</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'kb'</span> <span class="n" style="color: #333;">modifier</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">window</span> <span class="n" style="color: #333;">size</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kilobase</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">variant</span> <span class="k" style="font-weight: 600;">count</span></span>
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<td class="diff-line-num new new_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="mosel"><span class="n" style="color: #333;">units</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Pre</span><span class="p">\-</span><span class="s1" style="color: #d14;">'kb'</span> <span class="n" style="color: #333;">space</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="p">.</span> <span class="s2" style="color: #d14;">"\-\-indep\-pairwise 500 kb 5 0.5"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="s2" style="color: #d14;">"\-\-indep\-pairwise 500kb 5 0.5"</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">effect</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="mosel"><span class="n" style="color: #333;">Note</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">need</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">rerun</span> <span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">using</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">extract</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">or</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">exclude</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="mosel"><span class="p">\&.</span><span class="n" style="color: #333;">prune</span><span class="p">.</span><span class="k" style="font-weight: 600;">in</span><span class="p">/.</span><span class="n" style="color: #333;">prune</span><span class="p">.</span><span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">apply</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">another</span> <span class="n" style="color: #333;">computation</span><span class="p">.</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">r</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[{</span><span class="n" style="color: #333;">square</span> <span class="p">|</span> <span class="n" style="color: #333;">square0</span> <span class="p">|</span> <span class="n" style="color: #333;">triangle</span> <span class="p">|</span> <span class="k" style="font-weight: 600;">inter</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="p">}]</span> <span class="p">[{</span><span class="n" style="color: #333;">gz</span> <span class="p">|</span> <span class="n" style="color: #333;">bin</span> <span class="p">|</span> <span class="n" style="color: #333;">bin4</span><span class="p">}]</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'spaces'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'in\-phase'</span><span class="p">]</span> <span class="p">[{</span><span class="n" style="color: #333;">d</span> <span class="p">|</span> <span class="n" style="color: #333;">dprime</span> <span class="p">|</span> <span class="n" style="color: #333;">dprime</span><span class="p">\-</span><span class="n" style="color: #333;">signed</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'with\-freqs'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'yes\-really'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">r2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[{</span><span class="n" style="color: #333;">square</span> <span class="p">|</span> <span class="n" style="color: #333;">square0</span> <span class="p">|</span> <span class="n" style="color: #333;">triangle</span> <span class="p">|</span> <span class="k" style="font-weight: 600;">inter</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="p">}]</span> <span class="p">[{</span><span class="n" style="color: #333;">gz</span> <span class="p">|</span> <span class="n" style="color: #333;">bin</span> <span class="p">|</span> <span class="n" style="color: #333;">bin4</span><span class="p">}]</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'spaces'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'in\-phase'</span><span class="p">]</span> <span class="p">[{</span><span class="n" style="color: #333;">d</span> <span class="p">|</span> <span class="n" style="color: #333;">dprime</span> <span class="p">|</span> <span class="n" style="color: #333;">dprime</span><span class="p">\-</span><span class="n" style="color: #333;">signed</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'with\-freqs'</span><span class="p">]</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'yes\-really'</span><span class="p">]</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="mosel"><span class="n" style="color: #333;">LD</span> <span class="n" style="color: #333;">statistic</span> <span class="n" style="color: #333;">reports</span><span class="p">.</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">r</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">yields</span> <span class="n" style="color: #333;">raw</span> <span class="k" style="font-weight: 600;">inter</span><span class="p">\-</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">correlations</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">r2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">reports</span> <span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">squares</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="mosel"><span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">request</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">pairs</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="mosel"><span class="n" style="color: #333;">matrix</span> <span class="n" style="color: #333;">format</span> <span class="p">(</span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">specify</span> <span class="s1" style="color: #d14;">'bin'</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">shape</span> <span class="n" style="color: #333;">modifiers</span><span class="p">),</span> <span class="n" style="color: #333;">all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="mosel"><span class="n" style="color: #333;">pairs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span> <span class="n" style="color: #333;">format</span> <span class="p">(</span><span class="s1" style="color: #d14;">'inter\-chr'</span><span class="p">),</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">limited</span> <span class="n" style="color: #333;">window</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span> <span class="n" style="color: #333;">format</span></span>
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<td class="diff-line-num new new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">).</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'gz'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">gzipped</span><span class="p">.</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'bin'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">matrix</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">written</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">double</span><span class="p">\-</span><span class="n" style="color: #333;">precision</span> <span class="n" style="color: #333;">binary</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="mosel"><span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="s1" style="color: #d14;">'bin4'</span> <span class="n" style="color: #333;">specifics</span> <span class="n" style="color: #333;">single</span><span class="p">\-</span><span class="n" style="color: #333;">precision</span> <span class="n" style="color: #333;">binary</span><span class="p">.</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">matrix</span> <span class="n" style="color: #333;">is</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="mosel"><span class="n" style="color: #333;">square</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">shape</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">explicitly</span> <span class="n" style="color: #333;">specified</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">matrices</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">tab</span><span class="p">\-</span><span class="n" style="color: #333;">delimited</span><span class="p">;</span> <span class="s1" style="color: #d14;">'spaces'</span> <span class="n" style="color: #333;">switches</span> <span class="n" style="color: #333;">this</span><span class="p">.</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'in\-phase'</span> <span class="n" style="color: #333;">adds</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">with</span> <span class="k" style="font-weight: 600;">in</span><span class="p">\-</span><span class="n" style="color: #333;">phase</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">pairs</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">table</span><span class="p">\-</span><span class="n" style="color: #333;">formatted</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="mosel"><span class="n" style="color: #333;">reports</span><span class="p">.</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">long</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">codes</span><span class="p">.)</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'dprime'</span> <span class="n" style="color: #333;">adds</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">absolute</span> <span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Lewontin</span><span class="s1" style="color: #d14;">'s D\-prime statistic to</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="mosel"><span class="s1" style="color: #d14;">table\-formatted reports, and forces both r/r^2 and D\-prime to be based on</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="mosel"><span class="s1" style="color: #d14;">the maximum likelihood solution to the cubic equation discussed in Gaunt</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="mosel"><span class="s1" style="color: #d14;">T, Rodriguez S, Day I (2007) Cubic exact solutions for the estimation of</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="mosel"><span class="s1" style="color: #d14;">pairwise haplotype frequencies.</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">dprime</span><span class="p">\-</span><span class="n" style="color: #333;">signed</span><span class="s1" style="color: #d14;">' keeps the sign, while '</span><span class="n" style="color: #333;">d</span><span class="s1" style="color: #d14;">' skips division by D_{max}.</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="k" style="font-weight: 600;">with</span><span class="p">\-</span><span class="n" style="color: #333;">freqs</span><span class="s1" style="color: #d14;">' adds MAF columns to table\-formatted reports.</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Since the resulting file can easily be huge, you'</span><span class="n" style="color: #333;">re</span> <span class="n" style="color: #333;">required</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">add</span> <span class="n" style="color: #333;">the</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'yes\-really'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">requesting</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">unfiltered</span><span class="p">,</span> <span class="n" style="color: #333;">non</span><span class="p">\-</span><span class="n" style="color: #333;">distributed</span> <span class="n" style="color: #333;">all</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="mosel"><span class="n" style="color: #333;">pairs</span> <span class="n" style="color: #333;">computation</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">400</span><span class="n" style="color: #333;">k</span> <span class="n" style="color: #333;">variants</span><span class="p">.</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">computations</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">subdivided</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">parallel</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">(</span><span class="n" style="color: #333;">even</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'square'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">active</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">ld</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ID</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ID</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'hwe\-midp'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">displays</span> <span class="n" style="color: #333;">haplotype</span> <span class="n" style="color: #333;">frequencies</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">^</span><span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">D</span><span class="s1" style="color: #d14;">' for a single pair of</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="mosel"><span class="s1" style="color: #d14;">variants. When there are multiple biologically possible solutions to the</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="mosel"><span class="s1" style="color: #d14;">haplotype frequency cubic equation, all are displayed (instead of just the</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="mosel"><span class="s1" style="color: #d14;">maximum likelihood solution identified by \fB\-\-r\fR/\-\-r2), along with HWE exact</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="mosel"><span class="s1" style="color: #d14;">test statistics.</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-show\-tags\fR <filename></span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-show\-tags\fR all</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="mosel"><span class="s1" style="color: #d14;">* If a file is specified, list all variants which tag at least one variant</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="mosel"><span class="s1" style="color: #d14;">named in the file.</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="mosel"><span class="s1" style="color: #d14;">(This will normally be a superset of the original</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="mosel"><span class="s1" style="color: #d14;">list, since a variant is considered to tag itself here.)</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="mosel"><span class="s1" style="color: #d14;">* If '</span><span class="n" style="color: #333;">all</span><span class="s1" style="color: #d14;">' mode is specified, for each variant, each *other* variant which</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="mosel"><span class="s1" style="color: #d14;">tags it is reported.</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-blocks\fR ['</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\-</span><span class="n" style="color: #333;">req</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">small</span><span class="p">\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">\-</span><span class="n" style="color: #333;">span</span><span class="s1" style="color: #d14;">']</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="mosel"><span class="s1" style="color: #d14;">Estimate haplotype blocks, via Haploview'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">interpretation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">block</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="mosel"><span class="n" style="color: #333;">definition</span> <span class="n" style="color: #333;">suggested</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">Gabriel</span> <span class="n" style="color: #333;">S</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="p">(</span><span class="m" style="color: #099;">2002</span><span class="p">)</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">Structure</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Haplotype</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="mosel"><span class="n" style="color: #333;">Blocks</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Human</span> <span class="n" style="color: #333;">Genome</span><span class="p">.</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Normally</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">phenotypes</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">considered</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">this</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="mosel"><span class="n" style="color: #333;">computation</span><span class="p">;</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'no\-pheno\-req'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">lifts</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">restriction</span><span class="p">.</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Normally</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">\-</span><span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">blocks</span> <span class="n" style="color: #333;">may</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">span</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">20</span><span class="n" style="color: #333;">kb</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">size</span><span class="p">\-</span><span class="m" style="color: #099;">3</span> <span class="n" style="color: #333;">blocks</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">limited</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">30</span><span class="n" style="color: #333;">kb</span><span class="p">.</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'no\-small\-max\-span'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">removes</span> <span class="n" style="color: #333;">these</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="mosel"><span class="n" style="color: #333;">limits</span><span class="p">.</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="p">.</span><span class="n" style="color: #333;">blocks</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">valid</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">PLINK</span> <span class="m" style="color: #099;">1.07</span><span class="s1" style="color: #d14;">'s \fB\-\-hap\fR command.</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="mosel"><span class="s1" style="color: #d14;">However,</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="mosel"><span class="s1" style="color: #d14;">the \fB\-\-hap\fR... family of flags has not been reimplemented in PLINK 1.9 due to</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="mosel"><span class="s1" style="color: #d14;">poor phasing accuracy relative to other software; for now, we recommend</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="mosel"><span class="s1" style="color: #d14;">using BEAGLE instead of PLINK for case/control haplotype association</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="mosel"><span class="s1" style="color: #d14;">analysis. (You can use "\-\-recode beagle" to export data to BEAGLE 3.3.)</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="mosel"><span class="s1" style="color: #d14;">We apologize for the inconvenience, and plan to develop variants of the</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-hap\fR... flags which handle pre\-phased data effectively.</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-distance\fR [{square | square0 | triangle}] [{gz | bin | bin4}] ['</span><span class="n" style="color: #333;">ibs</span><span class="s1" style="color: #d14;">']</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="mosel"><span class="s1" style="color: #d14;">['</span><span class="m" style="color: #099;">1</span><span class="p">\-</span><span class="n" style="color: #333;">ibs</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">allele</span><span class="p">\-</span><span class="n" style="color: #333;">ct</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">flat</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="s1" style="color: #d14;">']</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="mosel"><span class="s1" style="color: #d14;">Write a lower\-triangular tab\-delimited table of (weighted) genomic</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="mosel"><span class="s1" style="color: #d14;">distances in allele count units to <output prefix>.dist, and a list of the</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="mosel"><span class="s1" style="color: #d14;">corresponding sample IDs to <output prefix>.dist.id. The first row of the</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&.dist file contains a single <genome 1\-genome 2> distance, the second row</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="mosel"><span class="s1" style="color: #d14;">has the <genome 1\-genome 3> and <genome 2\-genome 3> distances in that</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="mosel"><span class="s1" style="color: #d14;">order, etc.</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="mosel"><span class="s1" style="color: #d14;">* It is usually best to perform this calculation on a marker set in</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="mosel"><span class="s1" style="color: #d14;">approximate linkage equilibrium.</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="mosel"><span class="s1" style="color: #d14;">* If the '</span><span class="n" style="color: #333;">square</span><span class="s1" style="color: #d14;">' or '</span><span class="n" style="color: #333;">square0</span><span class="s1" style="color: #d14;">' modifier is present, a square matrix is</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="mosel"><span class="s1" style="color: #d14;">written instead; '</span><span class="n" style="color: #333;">square0</span><span class="s1" style="color: #d14;">' fills the upper right triangle with zeroes.</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="mosel"><span class="s1" style="color: #d14;">* If the '</span><span class="n" style="color: #333;">gz</span><span class="s1" style="color: #d14;">' modifier is present, a compressed .dist.gz file is written</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="mosel"><span class="s1" style="color: #d14;">instead of a plain text file.</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="mosel"><span class="s1" style="color: #d14;">* If the '</span><span class="n" style="color: #333;">bin</span><span class="s1" style="color: #d14;">' modifier is present, a binary (square) matrix of</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="mosel"><span class="s1" style="color: #d14;">double\-precision floating point values, suitable for loading from R, is</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="mosel"><span class="s1" style="color: #d14;">instead written to <output prefix>.dist.bin. ('</span><span class="n" style="color: #333;">bin4</span><span class="s1" style="color: #d14;">' specifies</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="mosel"><span class="s1" style="color: #d14;">single\-precision numbers instead.) This can be combined with '</span><span class="n" style="color: #333;">square0</span><span class="s1" style="color: #d14;">'</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="mosel"><span class="s1" style="color: #d14;">if you still want the upper right zeroed out, or '</span><span class="n" style="color: #333;">triangle</span><span class="s1" style="color: #d14;">' if you don'</span><span class="n" style="color: #333;">t</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="mosel"><span class="n" style="color: #333;">want</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">pad</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">upper</span> <span class="n" style="color: #333;">right</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">all</span><span class="p">.</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'ibs'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">present</span><span class="p">,</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">identity</span><span class="p">\-</span><span class="n" style="color: #333;">by</span><span class="p">\-</span><span class="n" style="color: #333;">state</span> <span class="n" style="color: #333;">matrix</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">written</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">prefix</span><span class="p">>.</span><span class="n" style="color: #333;">mibs</span><span class="p">.</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'1\-ibs'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">distances</span> <span class="n" style="color: #333;">expressed</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">genomic</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="mosel"><span class="n" style="color: #333;">proportions</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="p">.</span> <span class="m" style="color: #099;">1</span> <span class="p">\-</span> <span class="n" style="color: #333;">IBS</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">written</span> <span class="k" style="font-weight: 600;">to</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">prefix</span><span class="p">>.</span><span class="n" style="color: #333;">mdist</span><span class="p">.</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="mosel"><span class="n" style="color: #333;">Combine</span> <span class="k" style="font-weight: 600;">with</span> <span class="s1" style="color: #d14;">'allele\-ct'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">want</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">generate</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">usual</span> <span class="p">.</span><span class="n" style="color: #333;">dist</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">as</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="mosel"><span class="n" style="color: #333;">well</span><span class="p">.</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span> <span class="n" style="color: #333;">rescaling</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">presence</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">calls</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">sensitive</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">allele</span> <span class="k" style="font-weight: 600;">count</span> <span class="n" style="color: #333;">distributions</span><span class="p">:</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">contributes</span><span class="p">,</span> <span class="n" style="color: #333;">on</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="mosel"><span class="n" style="color: #333;">average</span><span class="p">,</span> <span class="n" style="color: #333;">twice</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">much</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">distances</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">B</span><span class="p">,</span> <span class="n" style="color: #333;">a</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="mosel"><span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">call</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">result</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">twice</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">large</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">missingness</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="mosel"><span class="n" style="color: #333;">correction</span><span class="p">.</span> <span class="k" style="font-weight: 600;">To</span> <span class="n" style="color: #333;">turn</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">off</span> <span class="p">(</span><span class="n" style="color: #333;">because</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">calls</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">highly</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="mosel"><span class="n" style="color: #333;">nonrandom</span><span class="p">),</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'flat\-missing'</span> <span class="n" style="color: #333;">modifier</span><span class="p">.</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">computation</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">subdivided</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">parallel</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">distance</span><span class="p">\-</span><span class="n" style="color: #333;">matrix</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">ibs</span><span class="p">\-</span><span class="n" style="color: #333;">matrix</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="mosel"><span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">deprecated</span> <span class="n" style="color: #333;">commands</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">equivalent</span> <span class="k" style="font-weight: 600;">to</span> <span class="s2" style="color: #d14;">"\-\-distance 1\-ibs flat\-missing</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="mosel"><span class="s2" style="color: #d14;">square"</span> <span class="k" style="font-weight: 600;">and</span> <span class="s2" style="color: #d14;">"\-\-distance ibs flat\-missing square"</span><span class="p">,</span> <span class="n" style="color: #333;">respectively</span><span class="p">,</span> <span class="n" style="color: #333;">except</span> <span class="n" style="color: #333;">that</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="mosel"><span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">generate</span> <span class="n" style="color: #333;">space</span><span class="p">\-</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">tab</span><span class="p">\-</span><span class="n" style="color: #333;">delimited</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">rel</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[{</span><span class="n" style="color: #333;">square</span> <span class="p">|</span> <span class="n" style="color: #333;">square0</span> <span class="p">|</span> <span class="n" style="color: #333;">triangle</span><span class="p">}]</span> <span class="p">[{</span><span class="n" style="color: #333;">gz</span> <span class="p">|</span> <span class="n" style="color: #333;">bin</span> <span class="p">|</span> <span class="n" style="color: #333;">bin4</span><span class="p">}]</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">cov</span> <span class="p">|</span> <span class="n" style="color: #333;">ibc2</span> <span class="p">|</span> <span class="n" style="color: #333;">ibc3</span><span class="p">}]</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="mosel"><span class="n" style="color: #333;">Write</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">lower</span><span class="p">\-</span><span class="n" style="color: #333;">triangular</span> <span class="n" style="color: #333;">variance</span><span class="p">\-</span><span class="n" style="color: #333;">standardized</span> <span class="n" style="color: #333;">realized</span> <span class="n" style="color: #333;">relationship</span> <span class="n" style="color: #333;">matrix</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">prefix</span><span class="p">>.</span><span class="n" style="color: #333;">rel</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">corresponding</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">to</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">prefix</span><span class="p">>.</span><span class="n" style="color: #333;">rel</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">.</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">usually</span> <span class="n" style="color: #333;">best</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">perform</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">marker</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">in</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="mosel"><span class="n" style="color: #333;">approximate</span> <span class="n" style="color: #333;">linkage</span> <span class="n" style="color: #333;">equilibrium</span><span class="p">.</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'square'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'square0'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'triangle'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'gz'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'bin'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'bin4'</span> <span class="n" style="color: #333;">act</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">they</span> <span class="k" style="font-weight: 600;">do</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="mosel"><span class="n" style="color: #333;">on</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">distance</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'cov'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">removes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variance</span> <span class="n" style="color: #333;">standardization</span> <span class="n" style="color: #333;">step</span><span class="p">,</span> <span class="n" style="color: #333;">causing</span> <span class="n" style="color: #333;">a</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="mosel"><span class="n" style="color: #333;">covariance</span> <span class="n" style="color: #333;">matrix</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">calculated</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">diagonal</span> <span class="n" style="color: #333;">elements</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">relationship</span> <span class="n" style="color: #333;">matrix</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">ibc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="s1" style="color: #d14;">'s Fhat1; use the '</span><span class="n" style="color: #333;">ibc2</span><span class="s1" style="color: #d14;">' or '</span><span class="n" style="color: #333;">ibc3</span><span class="s1" style="color: #d14;">' modifiers to base them on Fhat2</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="mosel"><span class="s1" style="color: #d14;">or Fhat3 instead.</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The computation can be subdivided with \fB\-\-parallel\fR.</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-make\-grm\-gz\fR ['</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">gz</span><span class="s1" style="color: #d14;">'] [{cov | ibc2 | ibc3}]</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-make\-grm\-bin\fR [{cov | ibc2 | ibc3}]</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-make\-grm\-gz\fR writes the relationships in GCTA'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">original</span> <span class="n" style="color: #333;">gzipped</span> <span class="k" style="font-weight: 600;">list</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="mosel"><span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">describes</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">pair</span> <span class="n" style="color: #333;">per</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">grm</span><span class="p">\-</span><span class="n" style="color: #333;">bin</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">writes</span> <span class="n" style="color: #333;">them</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">GCTA</span> <span class="m" style="color: #099;">1.1</span><span class="p">+</span><span class="s1" style="color: #d14;">'s single\-precision triangular binary format. Note that these</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="mosel"><span class="s1" style="color: #d14;">formats explicitly report the number of valid observations (where neither</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="mosel"><span class="s1" style="color: #d14;">sample has a missing call) for each pair, which is useful input for some</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="mosel"><span class="s1" style="color: #d14;">scripts.</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="mosel"><span class="s1" style="color: #d14;">These computations can be subdivided with \fB\-\-parallel\fR.</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-rel\-cutoff\fR [val]</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="mosel"><span class="s1" style="color: #d14;">(alias: \fB\-\-grm\-cutoff\fR)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="mosel"><span class="s1" style="color: #d14;">Exclude one member of each pair of samples with relatedness greater than</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="mosel"><span class="s1" style="color: #d14;">the given cutoff value (default 0.025). If no later operation will cause</span></span>
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<td class="diff-line-num new new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="mosel"><span class="s1" style="color: #d14;">the list of remaining samples to be written to disk, this will save it to</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="mosel"><span class="s1" style="color: #d14;"><output prefix>.rel.id.</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="mosel"><span class="s1" style="color: #d14;">Note that maximizing the remaining sample size is equivalent to the NP\-hard</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="mosel"><span class="s1" style="color: #d14;">maximum independent set problem, so we use a greedy algorithm instead of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="mosel"><span class="s1" style="color: #d14;">guaranteeing optimality. (Use the \fB\-\-make\-rel\fR and \fB\-\-keep\fR/\-\-remove flags if</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="mosel"><span class="s1" style="color: #d14;">you want to try to do better.)</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ibs\-test\fR [permutation count]</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-groupdist\fR [iters] [d]</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="mosel"><span class="s1" style="color: #d14;">Given case/control phenotype data, these commands consider three subsets of</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="mosel"><span class="s1" style="color: #d14;">the distance matrix: pairs of affected samples, affected\-unaffected pairs,</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="mosel"><span class="s1" style="color: #d14;">and pairs of unaffected samples. Each of these subsets has a distribution</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="mosel"><span class="s1" style="color: #d14;">of pairwise genomic distances; \fB\-\-ibs\-test\fR uses permutation to estimate</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="mosel"><span class="s1" style="color: #d14;">p\-values re: which types of pairs are most similar, while \fB\-\-groupdist\fR</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="mosel"><span class="s1" style="color: #d14;">focuses on the differences between the centers of these distributions and</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="mosel"><span class="s1" style="color: #d14;">estimates standard errors via delete\-d jackknife.</span></span>
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-regress\-distance\fR [iters] [d]</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="mosel"><span class="s1" style="color: #d14;">Linear regression of pairwise genomic distances on pairwise average</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="mosel"><span class="s1" style="color: #d14;">phenotypes and vice versa, using delete\-d jackknife for standard errors. A</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="mosel"><span class="s1" style="color: #d14;">scalar phenotype is required.</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="mosel"><span class="s1" style="color: #d14;">* With less than two parameters, d is set to <number of people>^0.6 rounded</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="mosel"><span class="s1" style="color: #d14;">down.</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="mosel"><span class="s1" style="color: #d14;">With no parameters, 100k iterations are run.</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-regress\-rel\fR [iters] [d]</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="mosel"><span class="s1" style="color: #d14;">Linear regression of pairwise genomic relationships on pairwise average</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="mosel"><span class="s1" style="color: #d14;">phenotypes, and vice versa. Defaults for iters and d are the same as for</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-regress\-distance\fR.</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-genome\fR ['</span><span class="n" style="color: #333;">gz</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">rel</span><span class="p">\-</span><span class="n" style="color: #333;">check</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">full</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">unbounded</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">nudge</span><span class="s1" style="color: #d14;">']</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="mosel"><span class="s1" style="color: #d14;">Generate an identity\-by\-descent report.</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="mosel"><span class="s1" style="color: #d14;">* It is usually best to perform this calculation on a marker set in</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="mosel"><span class="s1" style="color: #d14;">approximate linkage equilibrium.</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The '</span><span class="n" style="color: #333;">rel</span><span class="p">\-</span><span class="n" style="color: #333;">check</span><span class="s1" style="color: #d14;">' modifier excludes pairs of samples with different FIDs</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="mosel"><span class="s1" style="color: #d14;">from the final report.</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">full</span><span class="s1" style="color: #d14;">' adds raw pairwise comparison data to the report.</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The P(IBD=0/1/2) estimator employed by this command sometimes yields</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="mosel"><span class="s1" style="color: #d14;">numbers outside the range [0,1]; by default, these are clipped.</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="mosel"><span class="s1" style="color: #d14;">The</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">unbounded</span><span class="s1" style="color: #d14;">' modifier turns off this clipping.</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Then, when PI_HAT^2 < P(IBD=2), '</span><span class="n" style="color: #333;">nudge</span><span class="s1" style="color: #d14;">' adjusts the final P(IBD=0/1/2)</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="mosel"><span class="s1" style="color: #d14;">estimates to a theoretically possible configuration.</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The computation can be subdivided with \fB\-\-parallel\fR.</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\fR [{group | group\-verbose}] ['</span><span class="n" style="color: #333;">consensus</span><span class="p">\-</span><span class="n" style="color: #333;">match</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">extend</span><span class="s1" style="color: #d14;">']</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="mosel"><span class="s1" style="color: #d14;">['</span><span class="n" style="color: #333;">subtract</span><span class="p">\-</span><span class="m" style="color: #099;">1</span><span class="p">\-</span><span class="k" style="font-weight: 600;">from</span><span class="p">\-</span><span class="n" style="color: #333;">lengths</span><span class="s1" style="color: #d14;">']</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-snp\fR <min var count></span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-kb\fR <min length></span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-density\fR <max inverse density (kb/var)></span></span>
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<td class="diff-line-num new new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-gap\fR <max internal gap kb length></span></span>
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<td class="diff-line-num new new_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-het\fR <max hets></span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-window\-snp\fR <scanning window size></span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-window\-het\fR <max hets in scanning window hit></span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-window\-missing\fR <max missing calls in scanning window hit></span></span>
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<td class="diff-line-num new new_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-window\-threshold\fR <min scanning window hit rate></span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="mosel"><span class="s1" style="color: #d14;">These commands request a set of run\-of\-homozygosity reports, and allow you</span></span>
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<td class="diff-line-num new new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="mosel"><span class="s1" style="color: #d14;">to customize how they are generated.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="mosel"><span class="s1" style="color: #d14;">* If you'</span><span class="n" style="color: #333;">re</span> <span class="n" style="color: #333;">satisfied</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">settings</span> <span class="n" style="color: #333;">described</span> <span class="n" style="color: #333;">below</span><span class="p">,</span> <span class="n" style="color: #333;">just</span></span>
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<td class="diff-line-num new new_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="mosel"><span class="n" style="color: #333;">use</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">modifiers</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="mosel"><span class="n" style="color: #333;">Otherwise</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">lets</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="mosel"><span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">binary</span> <span class="n" style="color: #333;">settings</span><span class="p">:</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'group[\-verbose]'</span> <span class="n" style="color: #333;">adds</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">pools</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">overlapping</span> <span class="n" style="color: #333;">runs</span> <span class="k" style="font-weight: 600;">of</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="mosel"><span class="n" style="color: #333;">homozygosity</span><span class="p">.</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">Automatically</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">when</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">match</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">present</span><span class="p">.)</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">With</span> <span class="s1" style="color: #d14;">'group[\-verbose]'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'consensus\-match'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">segmental</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="mosel"><span class="n" style="color: #333;">matches</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">called</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">pool</span><span class="s1" style="color: #d14;">'s consensus</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="mosel"><span class="s1" style="color: #d14;">segment, rather than the variants in the pairwise intersection.</span></span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Due to how the scanning window algorithm works, it is possible for a</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="mosel"><span class="s1" style="color: #d14;">reported ROH to be adjacent to a few homozygous variants.</span></span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="mosel"><span class="s1" style="color: #d14;">The '</span><span class="n" style="color: #333;">extend</span><span class="s1" style="color: #d14;">'</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="mosel"><span class="s1" style="color: #d14;">modifier causes them to be included in the reported ROH if that</span></span>
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<td class="diff-line-num new new_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="mosel"><span class="s1" style="color: #d14;">wouldn'</span><span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">cause</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">violation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">density</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">bound</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">segment</span> <span class="n" style="color: #333;">bp</span> <span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">calculated</span> <span class="k" style="font-weight: 600;">as</span> <span class="p"><</span><span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">bp</span> <span class="n" style="color: #333;">position</span><span class="p">></span> <span class="p">\-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">start</span> <span class="n" style="color: #333;">bp</span> <span class="n" style="color: #333;">position</span><span class="p">></span> <span class="p">+</span> <span class="m" style="color: #099;">1.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="mosel"><span class="n" style="color: #333;">Therefore</span><span class="p">,</span> <span class="n" style="color: #333;">reports</span> <span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">differ</span> <span class="n" style="color: #333;">slightly</span></span>
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<td class="diff-line-num new new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">PLINK</span> <span class="m" style="color: #099;">1.07</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">add</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">end</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="mosel"><span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">testing</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="mosel"><span class="n" style="color: #333;">purposes</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'subtract\-1\-from\-lengths'</span> <span class="n" style="color: #333;">modifier</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">apply</span></span>
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<td class="diff-line-num new new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">old</span> <span class="n" style="color: #333;">formula</span><span class="p">.</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">runs</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">homozygosity</span> <span class="n" style="color: #333;">containing</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">least</span> <span class="m" style="color: #099;">100</span> <span class="n" style="color: #333;">variants</span><span class="p">,</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">total</span> <span class="n" style="color: #333;">length</span> <span class="p">>=</span> <span class="m" style="color: #099;">1000</span> <span class="n" style="color: #333;">kilobases</span><span class="p">,</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">noted</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="mosel"><span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">these</span></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="mosel"><span class="n" style="color: #333;">minimums</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">kb</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">,</span> <span class="n" style="color: #333;">respectively</span><span class="p">.</span></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">ROH</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">least</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">per</span> <span class="m" style="color: #099;">50</span> <span class="n" style="color: #333;">kb</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">average</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="mosel"><span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">bound</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">density</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">consecutive</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">1000</span> <span class="n" style="color: #333;">kb</span> <span class="n" style="color: #333;">apart</span><span class="p">,</span> <span class="n" style="color: #333;">they</span></span>
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<td class="diff-line-num new new_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="mosel"><span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">be</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">ROH</span><span class="p">;</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">bound</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">gap</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">ROH</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">unlimited</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">heterozygous</span> <span class="n" style="color: #333;">calls</span><span class="p">;</span></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="mosel"><span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">impose</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">limit</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">het</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">scanning</span> <span class="n" style="color: #333;">window</span> <span class="n" style="color: #333;">contains</span> <span class="m" style="color: #099;">50</span> <span class="n" style="color: #333;">variants</span><span class="p">;</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">with</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">window</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">scanning</span> <span class="n" style="color: #333;">window</span> <span class="n" style="color: #333;">hit</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">most</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">heterozygous</span></span>
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<td class="diff-line-num new new_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="mosel"><span class="n" style="color: #333;">call</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">5</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">calls</span><span class="p">;</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">limits</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">window</span><span class="p">\-</span><span class="n" style="color: #333;">het</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">window</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">,</span> <span class="n" style="color: #333;">respectively</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variant</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">eligible</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">inclusion</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">ROH</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">hit</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="mosel"><span class="n" style="color: #333;">rate</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">scanning</span> <span class="n" style="color: #333;">windows</span> <span class="n" style="color: #333;">containing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">least</span></span>
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<td class="diff-line-num new new_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="mosel"><span class="m" style="color: #099;">0.05</span><span class="p">;</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">threshold</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homozyg</span><span class="p">\-</span><span class="n" style="color: #333;">window</span><span class="p">\-</span><span class="n" style="color: #333;">threshold</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">cluster</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'cc'</span><span class="p">]</span> <span class="p">[{</span><span class="n" style="color: #333;">group</span><span class="p">\-</span><span class="n" style="color: #333;">avg</span> <span class="p">|</span> <span class="n" style="color: #333;">old</span><span class="p">\-</span><span class="n" style="color: #333;">tiebreaks</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'missing'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'only2'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="mosel"><span class="n" style="color: #333;">Cluster</span> <span class="n" style="color: #333;">samples</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">similarity</span> <span class="n" style="color: #333;">statistic</span> <span class="p">(</span><span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">IBS</span><span class="p">).</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'cc'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">forces</span> <span class="n" style="color: #333;">every</span> <span class="n" style="color: #333;">cluster</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">least</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">case</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">one</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="mosel"><span class="n" style="color: #333;">control</span><span class="p">.</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'group\-avg'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">clusters</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">joined</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">average</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="mosel"><span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">minimum</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">similarity</span><span class="p">.</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'missing'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">clustering</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="mosel"><span class="n" style="color: #333;">identity</span><span class="p">\-</span><span class="n" style="color: #333;">by</span><span class="p">\-</span><span class="n" style="color: #333;">missingness</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">identity</span><span class="p">\-</span><span class="n" style="color: #333;">by</span><span class="p">\-</span><span class="n" style="color: #333;">state</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">writes</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="mosel"><span class="n" style="color: #333;">space</span><span class="p">\-</span><span class="n" style="color: #333;">delimited</span> <span class="n" style="color: #333;">identity</span><span class="p">\-</span><span class="n" style="color: #333;">by</span><span class="p">\-</span><span class="n" style="color: #333;">missingness</span> <span class="n" style="color: #333;">matrix</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">disk</span><span class="p">.</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'only2'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">a</span> <span class="p">.</span><span class="n" style="color: #333;">cluster2</span> <span class="n" style="color: #333;">file</span> <span class="p">(</span><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">valid</span> <span class="n" style="color: #333;">input</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">within</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">written</span><span class="p">;</span> <span class="n" style="color: #333;">otherwise</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">produced</span><span class="p">.</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">IBS</span> <span class="n" style="color: #333;">ties</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">broken</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">manner</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">PLINK</span> <span class="m" style="color: #099;">1.07</span><span class="p">,</span> <span class="n" style="color: #333;">so</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="mosel"><span class="n" style="color: #333;">final</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">solutions</span> <span class="n" style="color: #333;">tend</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">differ</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">generally</span> <span class="n" style="color: #333;">harmless</span><span class="p">.</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="mosel"><span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">simplify</span> <span class="n" style="color: #333;">testing</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'old\-tiebreaks'</span> <span class="n" style="color: #333;">modifier</span> <span class="k" style="font-weight: 600;">to</span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="mosel"><span class="n" style="color: #333;">force</span> <span class="n" style="color: #333;">emulation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">old</span> <span class="n" style="color: #333;">algorithm</span><span class="p">.</span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pca</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="k" style="font-weight: 600;">count</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'header'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'tabs'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'var\-wts'</span><span class="p">]</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="mosel"><span class="n" style="color: #333;">Calculates</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variance</span><span class="p">\-</span><span class="n" style="color: #333;">standardized</span> <span class="n" style="color: #333;">relationship</span> <span class="n" style="color: #333;">matrix</span> <span class="p">(</span><span class="n" style="color: #333;">use</span></span>
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<td class="diff-line-num new new_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">rel</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">grm</span><span class="p">\-</span><span class="n" style="color: #333;">gz</span><span class="p">/\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">grm</span><span class="p">\-</span><span class="n" style="color: #333;">bin</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">dump</span> <span class="n" style="color: #333;">it</span><span class="p">),</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">extracts</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">top</span></span>
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<td class="diff-line-num new new_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="mosel"><span class="m" style="color: #099;">20</span> <span class="n" style="color: #333;">principal</span> <span class="n" style="color: #333;">components</span><span class="p">.</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">usually</span> <span class="n" style="color: #333;">best</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">perform</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">marker</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">in</span></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="mosel"><span class="n" style="color: #333;">approximate</span> <span class="n" style="color: #333;">linkage</span> <span class="n" style="color: #333;">equilibrium</span><span class="p">.</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">PCs</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">passing</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">numeric</span> <span class="n" style="color: #333;">parameter</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'header'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">adds</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">header</span> <span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="p">.</span><span class="n" style="color: #333;">eigenvec</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">compatibility</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">GCTA</span> <span class="n" style="color: #333;">flag</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">no</span></span>
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<td class="diff-line-num new new_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="mosel"><span class="n" style="color: #333;">header</span> <span class="n" style="color: #333;">line</span><span class="p">.)</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'tabs'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="p">.</span><span class="n" style="color: #333;">eigenvec</span> <span class="n" style="color: #333;">file</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tab</span><span class="p">\-</span><span class="n" style="color: #333;">delimited</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'var\-wts'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">requests</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">additional</span> <span class="p">.</span><span class="n" style="color: #333;">eigenvec</span><span class="p">.</span><span class="n" style="color: #333;">var</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">PCs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="mosel"><span class="n" style="color: #333;">expressed</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">weights</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">weights</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">neighbour</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n1</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">n2</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">alias</span><span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">neighbor</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="mosel"><span class="n" style="color: #333;">Report</span> <span class="n" style="color: #333;">IBS</span> <span class="n" style="color: #333;">distances</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">sample</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">n1th</span><span class="p">\-</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">n2th</span><span class="p">\-</span><span class="n" style="color: #333;">nearest</span></span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="mosel"><span class="n" style="color: #333;">neighbors</span><span class="p">,</span> <span class="n" style="color: #333;">associated</span> <span class="n" style="color: #333;">Z</span><span class="p">\-</span><span class="n" style="color: #333;">scores</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">identities</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">neighbors</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="mosel"><span class="n" style="color: #333;">Useful</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">outlier</span> <span class="n" style="color: #333;">detection</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">assoc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm'</span> <span class="p">|</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm\-count'</span><span class="p">]</span> <span class="p">[{</span><span class="n" style="color: #333;">fisher</span> <span class="p">|</span> <span class="n" style="color: #333;">fisher</span><span class="p">\-</span><span class="n" style="color: #333;">midp</span><span class="p">}]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'counts'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'set\-test'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">assoc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm'</span> <span class="p">|</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm\-count'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'qt\-means'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'lin'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'set\-test'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">model</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm'</span> <span class="p">|</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm\-count'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">fisher</span> <span class="p">|</span> <span class="n" style="color: #333;">fisher</span><span class="p">\-</span><span class="n" style="color: #333;">midp</span> <span class="p">|</span> <span class="n" style="color: #333;">trend</span><span class="p">\-</span><span class="n" style="color: #333;">only</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'set\-test'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">dom</span> <span class="p">|</span> <span class="n" style="color: #333;">rec</span> <span class="p">|</span> <span class="n" style="color: #333;">gen</span> <span class="p">|</span> <span class="n" style="color: #333;">trend</span><span class="p">}]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="mosel"><span class="n" style="color: #333;">Basic</span> <span class="n" style="color: #333;">association</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="mosel"><span class="n" style="color: #333;">Given</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">phenotype</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">assoc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">performs</span> <span class="n" style="color: #333;">a</span> <span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">df</span> <span class="n" style="color: #333;">chi</span><span class="p">\-</span><span class="n" style="color: #333;">square</span> <span class="n" style="color: #333;">allelic</span></span>
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<td class="diff-line-num new new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="mosel"><span class="n" style="color: #333;">test</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">model</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">performs</span> <span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">tests</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span> <span class="p">(</span><span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">df</span> <span class="n" style="color: #333;">dominant</span> <span class="n" style="color: #333;">gene</span></span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="mosel"><span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">df</span> <span class="n" style="color: #333;">recessive</span> <span class="n" style="color: #333;">gene</span> <span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="m" style="color: #099;">2</span><span class="n" style="color: #333;">df</span> <span class="n" style="color: #333;">genotypic</span><span class="p">,</span> <span class="n" style="color: #333;">Cochran</span><span class="p">\-</span><span class="n" style="color: #333;">Armitage</span> <span class="n" style="color: #333;">trend</span><span class="p">).</span></span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">With</span> <span class="s1" style="color: #d14;">'fisher'</span><span class="p">/</span><span class="s1" style="color: #d14;">'fisher\-midp'</span><span class="p">,</span> <span class="n" style="color: #333;">Fisher</span><span class="s1" style="color: #d14;">'s exact test is used to generate</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="mosel"><span class="s1" style="color: #d14;">p\-values.</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">fisher</span><span class="p">\-</span><span class="n" style="color: #333;">midp</span><span class="s1" style="color: #d14;">' also applies Lancaster'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">mid</span><span class="p">\-</span><span class="n" style="color: #333;">p</span> <span class="n" style="color: #333;">adjustment</span><span class="p">.</span></span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'perm'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">adaptive</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">performed</span><span class="p">.</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">></span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">)</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">specified</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="mosel"><span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">replications</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">performed</span><span class="p">.</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'perm\-count'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">report</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">include</span> <span class="n" style="color: #333;">counts</span> <span class="n" style="color: #333;">instead</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="mosel"><span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">frequencies</span><span class="p">.</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'counts'</span> <span class="n" style="color: #333;">causes</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">assoc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">counts</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">frequencies</span><span class="p">.</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'set\-test'</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">significance</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">sets</span><span class="p">.</span> <span class="n" style="color: #333;">Requires</span> <span class="n" style="color: #333;">permutation</span><span class="p">;</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="mosel"><span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">customized</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">p</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">r2</span><span class="p">/\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'dom'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'rec'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'gen'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'trend'</span> <span class="n" style="color: #333;">force</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">corresponding</span> <span class="n" style="color: #333;">test</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span></span>
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<td class="diff-line-num new new_line" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="mosel"><span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">basis</span> <span class="n" style="color: #333;">for</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">model</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">permutation</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">most</span> <span class="n" style="color: #333;">significant</span></span>
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<td class="diff-line-num new new_line" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="mosel"><span class="n" style="color: #333;">result</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">allelic</span><span class="p">,</span> <span class="n" style="color: #333;">dominant</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">recessive</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">used</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'trend\-only'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">trend</span> <span class="n" style="color: #333;">test</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">performed</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="mosel"><span class="n" style="color: #333;">Given</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">quantitative</span> <span class="n" style="color: #333;">phenotype</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">assoc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">performs</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Wald</span> <span class="n" style="color: #333;">test</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">case</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'qt\-means'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">trait</span> <span class="n" style="color: #333;">means</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">standard</span></span>
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<td class="diff-line-num new new_line" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="mosel"><span class="n" style="color: #333;">deviations</span> <span class="n" style="color: #333;">stratified</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">genotype</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">reported</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'lin'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Lin</span> <span class="n" style="color: #333;">statistic</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">computed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">basis</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num new new_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="mosel"><span class="n" style="color: #333;">multiple</span><span class="p">\-</span><span class="n" style="color: #333;">testing</span> <span class="n" style="color: #333;">corrections</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">tests</span><span class="p">.</span></span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="mosel"><span class="n" style="color: #333;">Several</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">flags</span> <span class="p">(</span><span class="n" style="color: #333;">most</span> <span class="n" style="color: #333;">notably</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">aperm</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">customize</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="mosel"><span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span><span class="p">.</span></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mh</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm'</span> <span class="p">|</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm\-count'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'set\-test'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">alias</span><span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">cmh</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">bd</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm'</span> <span class="p">|</span> <span class="s1" style="color: #d14;">'perm\-bd'</span> <span class="p">|</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm\-count'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'set\-test'</span><span class="p">]</span></span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mh2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homog</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="mosel"><span class="n" style="color: #333;">Given</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">phenotype</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">clusters</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mh</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">computes</span> <span class="m" style="color: #099;">2</span><span class="n" style="color: #333;">x2xK</span></span>
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<td class="diff-line-num new new_line" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="mosel"><span class="n" style="color: #333;">Cochran</span><span class="p">\-</span><span class="n" style="color: #333;">Mantel</span><span class="p">\-</span><span class="n" style="color: #333;">Haenszel</span> <span class="n" style="color: #333;">statistics</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">variant</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">bd</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">also</span></span>
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<td class="diff-line-num new new_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="mosel"><span class="n" style="color: #333;">performs</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Breslow</span><span class="p">\-</span><span class="n" style="color: #333;">Day</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">odds</span> <span class="n" style="color: #333;">ratio</span> <span class="n" style="color: #333;">homogeneity</span><span class="p">.</span> <span class="n" style="color: #333;">Permutation</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num new new_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="mosel"><span class="n" style="color: #333;">variant</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">testing</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">CMH</span> <span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">)</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">Breslow</span><span class="p">\-</span><span class="n" style="color: #333;">Day</span> <span class="p">(</span><span class="n" style="color: #333;">when</span></span>
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<td class="diff-line-num new new_line" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'perm\-bd'</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">present</span><span class="p">)</span> <span class="n" style="color: #333;">statistic</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">supported</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">similar</span> <span class="n" style="color: #333;">analyses</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">available</span><span class="p">:</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="mosel"><span class="p">*</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mh2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">swaps</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">roles</span> <span class="k" style="font-weight: 600;">of</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">status</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">membership</span><span class="p">,</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="mosel"><span class="n" style="color: #333;">performing</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">phenotype</span><span class="p">\-</span><span class="n" style="color: #333;">stratified</span> <span class="n" style="color: #333;">IxJxK</span> <span class="n" style="color: #333;">Cochran</span><span class="p">\-</span><span class="n" style="color: #333;">Mantel</span><span class="p">\-</span><span class="n" style="color: #333;">Haenszel</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">on</span></span>
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<td class="diff-line-num new new_line" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="mosel"><span class="n" style="color: #333;">association</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">assignments</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">genotypes</span><span class="p">.</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="mosel"><span class="p">*</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">homog</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">executes</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">alternative</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Breslow</span><span class="p">\-</span><span class="n" style="color: #333;">Day</span> <span class="n" style="color: #333;">test</span><span class="p">,</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="mosel"><span class="n" style="color: #333;">partitioning</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">chi</span><span class="p">\-</span><span class="n" style="color: #333;">square</span> <span class="n" style="color: #333;">statistic</span><span class="p">.</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gxe</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">index</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="mosel"><span class="n" style="color: #333;">Given</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">quantitative</span> <span class="n" style="color: #333;">phenotype</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">loaded</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="mosel"><span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">defining</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">groups</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gxe</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">compares</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">regression</span> <span class="n" style="color: #333;">coefficient</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="mosel"><span class="n" style="color: #333;">derived</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">considering</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">members</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">group</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">regression</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="mosel"><span class="n" style="color: #333;">coefficient</span> <span class="n" style="color: #333;">derived</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">considering</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">members</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">other</span><span class="p">.</span> <span class="n" style="color: #333;">By</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="mosel"><span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">covariate</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">defines</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">groups</span><span class="p">;</span> <span class="n" style="color: #333;">use</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="mosel"><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="s2" style="color: #d14;">"\-\-gxe 3"</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">base</span> <span class="n" style="color: #333;">them</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">third</span> <span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">linear</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm'</span> <span class="p">|</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm\-count'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'set\-test'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">genotypic</span> <span class="p">|</span> <span class="n" style="color: #333;">hethom</span> <span class="p">|</span> <span class="n" style="color: #333;">dominant</span> <span class="p">|</span> <span class="n" style="color: #333;">recessive</span> <span class="p">|</span> <span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">}]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'hide\-covar'</span><span class="p">]</span> <span class="p">[{</span><span class="n" style="color: #333;">sex</span> <span class="p">|</span> <span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">x</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'interaction'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'beta'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'standard\-beta'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'intercept'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">logistic</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm'</span> <span class="p">|</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'perm\-count'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'set\-test'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">genotypic</span> <span class="p">|</span> <span class="n" style="color: #333;">hethom</span> <span class="p">|</span> <span class="n" style="color: #333;">dominant</span> <span class="p">|</span> <span class="n" style="color: #333;">recessive</span> <span class="p">|</span> <span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">}]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'hide\-covar'</span><span class="p">]</span> <span class="p">[{</span><span class="n" style="color: #333;">sex</span> <span class="p">|</span> <span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">x</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'interaction'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'beta'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'intercept'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="mosel"><span class="n" style="color: #333;">Multi</span><span class="p">\-</span><span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">association</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">quantitative</span> <span class="p">(\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">linear</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span> <span class="k" style="font-weight: 600;">or</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="mosel"><span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="p">(\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">logistic</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span> <span class="n" style="color: #333;">phenotype</span><span class="p">.</span> <span class="n" style="color: #333;">Normally</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'perm'</span> <span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">adaptive</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">performed</span> <span class="n" style="color: #333;">on</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">main</span> <span class="n" style="color: #333;">effect</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="s1" style="color: #d14;">'mperm='</span><span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">></span> <span class="n" style="color: #333;">starts</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">)</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span><span class="p">.</span></span>
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1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'perm\-count'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">report</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">include</span> <span class="n" style="color: #333;">counts</span> <span class="n" style="color: #333;">instead</span></span>
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1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="mosel"><span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">frequencies</span><span class="p">.</span></span>
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1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'set\-test'</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">significance</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">sets</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="mosel"><span class="n" style="color: #333;">Requires</span> <span class="n" style="color: #333;">permutation</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="mosel"><span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">customized</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">p</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">r2</span><span class="p">/\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">.</span></span>
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1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'genotypic'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">adds</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">additive</span> <span class="n" style="color: #333;">effect</span><span class="p">/</span><span class="n" style="color: #333;">dominance</span> <span class="n" style="color: #333;">deviation</span> <span class="m" style="color: #099;">2</span><span class="n" style="color: #333;">df</span></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="mosel"><span class="n" style="color: #333;">joint</span> <span class="n" style="color: #333;">test</span> <span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">/</span><span class="m" style="color: #099;">1</span><span class="p">/</span><span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">0</span><span class="p">/</span><span class="m" style="color: #099;">1</span><span class="p">/</span><span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">coding</span><span class="p">),</span> <span class="k" style="font-weight: 600;">while</span> <span class="s1" style="color: #d14;">'hethom'</span> <span class="k" style="font-weight: 600;">uses</span> <span class="m" style="color: #099;">0</span><span class="p">/</span><span class="m" style="color: #099;">0</span><span class="p">/</span><span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">0</span><span class="p">/</span><span class="m" style="color: #099;">1</span><span class="p">/</span><span class="m" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="mosel"><span class="n" style="color: #333;">coding</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">requested</span><span class="p">,</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">modifiers</span> <span class="n" style="color: #333;">cause</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="mosel"><span class="n" style="color: #333;">permutation</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">joint</span> <span class="n" style="color: #333;">test</span><span class="p">.</span></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'dominant'</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'recessive'</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">assuming</span> <span class="n" style="color: #333;">full</span> <span class="n" style="color: #333;">dominance</span> <span class="k" style="font-weight: 600;">or</span></span>
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1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="mosel"><span class="n" style="color: #333;">recessiveness</span><span class="p">,</span> <span class="n" style="color: #333;">respectively</span><span class="p">,</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">A1</span> <span class="n" style="color: #333;">allele</span><span class="p">.</span></span>
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1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'no\-snp'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">regression</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">performed</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">phenotype</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="mosel"><span class="n" style="color: #333;">covariates</span><span class="p">,</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">reference</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">genomic</span> <span class="n" style="color: #333;">data</span><span class="p">.</span></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">also</span></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="mosel"><span class="n" style="color: #333;">requested</span><span class="p">,</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">reported</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">covariates</span><span class="p">.</span></span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'hide\-covar'</span> <span class="n" style="color: #333;">removes</span> <span class="n" style="color: #333;">covariate</span><span class="p">\-</span><span class="n" style="color: #333;">specific</span> <span class="n" style="color: #333;">lines</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">sex</span> <span class="p">(</span><span class="n" style="color: #333;">male</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">female</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">automatically</span> <span class="n" style="color: #333;">added</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">a</span></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="mosel"><span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">X</span> <span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">variants</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nowhere</span> <span class="k" style="font-weight: 600;">else</span><span class="p">.</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'sex'</span> <span class="n" style="color: #333;">modifier</span></span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="mosel"><span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">it</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">everywhere</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="s1" style="color: #d14;">'no\-x\-sex'</span> <span class="n" style="color: #333;">excludes</span> <span class="n" style="color: #333;">it</span><span class="p">.</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'interaction'</span> <span class="n" style="color: #333;">adds</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">x</span> <span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">interactions</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span><span class="p">.</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="mosel"><span class="n" style="color: #333;">This</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="mosel"><span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">usual</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">tests</span><span class="p">;</span> <span class="n" style="color: #333;">use</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">tests</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">define</span></span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">statistic</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'intercept'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">intercepts</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">main</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">logistic</span> <span class="n" style="color: #333;">regressions</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'beta'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">regression</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="mosel"><span class="n" style="color: #333;">coefficients</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">odds</span> <span class="n" style="color: #333;">ratios</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">reported</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">With</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">linear</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'standard\-beta'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">standardizes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">phenotype</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">predictors</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">zero</span> <span class="n" style="color: #333;">mean</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">unit</span> <span class="n" style="color: #333;">variance</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">regression</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">dosage</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">dosage</span> <span class="n" style="color: #333;">file</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'noheader'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'skip0='</span><span class="p"><</span><span class="n" style="color: #333;">i</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'skip1='</span><span class="p"><</span><span class="n" style="color: #333;">j</span><span class="p">>]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'skip2='</span><span class="p"><</span><span class="n" style="color: #333;">k</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'dose1'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'format='</span><span class="p"><</span><span class="n" style="color: #333;">m</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'Zout'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">occur</span> <span class="p">|</span> <span class="n" style="color: #333;">standard</span><span class="p">\-</span><span class="n" style="color: #333;">beta</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'sex'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'case\-control\-freqs'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">dosage</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">file</span><span class="p">></span> <span class="k" style="font-weight: 600;">list</span> <span class="p">[{</span><span class="n" style="color: #333;">sepheader</span> <span class="p">|</span> <span class="n" style="color: #333;">noheader</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'skip0='</span><span class="p"><</span><span class="n" style="color: #333;">i</span><span class="p">>]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'skip1='</span><span class="p"><</span><span class="n" style="color: #333;">j</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'skip2='</span><span class="p"><</span><span class="n" style="color: #333;">k</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'dose1'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'format='</span><span class="p"><</span><span class="n" style="color: #333;">m</span><span class="p">>]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'Zout'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">occur</span> <span class="p">|</span> <span class="n" style="color: #333;">standard</span><span class="p">\-</span><span class="n" style="color: #333;">beta</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'sex'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'case\-control\-freqs'</span><span class="p">]</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">dosage</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="mosel"><span class="n" style="color: #333;">Process</span> <span class="p">(</span><span class="n" style="color: #333;">possibly</span> <span class="n" style="color: #333;">gzipped</span><span class="p">)</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">variant</span><span class="p">\-</span><span class="n" style="color: #333;">major</span> <span class="n" style="color: #333;">allelic</span> <span class="n" style="color: #333;">dosage</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="mosel"><span class="n" style="color: #333;">data</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">regular</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">fileset</span><span class="p">;</span> <span class="n" style="color: #333;">instead</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">must</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="mosel"><span class="p">*</span><span class="n" style="color: #333;">only</span><span class="p">*</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">a</span> <span class="p">.</span><span class="n" style="color: #333;">fam</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">possibly</span> <span class="n" style="color: #333;">a</span> <span class="p">.</span><span class="n" style="color: #333;">map</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span><span class="s1" style="color: #d14;">'t specify any</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="mosel"><span class="s1" style="color: #d14;">other commands.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="mosel"><span class="s1" style="color: #d14;">* PLINK 2.0 will have first\-class support for genotype probabilities. An</span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="mosel"><span class="s1" style="color: #d14;">equivalent data import flag will be provided then, and \fB\-\-dosage\fR will be</span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="mosel"><span class="s1" style="color: #d14;">retired.</span></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="mosel"><span class="s1" style="color: #d14;">* By default, \fB\-\-dosage\fR assumes that only one allelic dosage file should be</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="mosel"><span class="s1" style="color: #d14;">loaded.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="mosel"><span class="s1" style="color: #d14;">To specify multiple files,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="mosel"><span class="s1" style="color: #d14;">1. create a master list with one entry per line.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="mosel"><span class="s1" style="color: #d14;">There are normally two</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="mosel"><span class="s1" style="color: #d14;">supported formats for this list: just a filename per line, or variant</span></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="mosel"><span class="s1" style="color: #d14;">batch numbers in the first column and filenames in the second.</span></span>
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="mosel"><span class="s1" style="color: #d14;">2. Provide the name of that list as the first \fB\-\-dosage\fR parameter.</span></span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="mosel"><span class="s1" style="color: #d14;">3. Add the '</span><span class="k" style="font-weight: 600;">list</span><span class="s1" style="color: #d14;">' modifier.</span></span>
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1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="mosel"><span class="s1" style="color: #d14;">* By default, \fB\-\-dosage\fR assumes the allelic dosage file(s) contain a header</span></span>
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1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="mosel"><span class="s1" style="color: #d14;">line, which has '</span><span class="n" style="color: #333;">SNP</span><span class="s1" style="color: #d14;">' in column i+1, '</span><span class="n" style="color: #333;">A1</span><span class="s1" style="color: #d14;">' in column i+j+2, '</span><span class="n" style="color: #333;">A2</span><span class="s1" style="color: #d14;">' in column</span></span>
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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="mosel"><span class="s1" style="color: #d14;">i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are</span></span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="mosel"><span class="s1" style="color: #d14;">normally zero, but can be changed with '</span><span class="n" style="color: #333;">skip0</span><span class="s1" style="color: #d14;">', '</span><span class="n" style="color: #333;">skip1</span><span class="s1" style="color: #d14;">', and '</span><span class="n" style="color: #333;">skip2</span><span class="s1" style="color: #d14;">'</span></span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="mosel"><span class="s1" style="color: #d14;">respectively.) If such a header line is not present,</span></span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="mosel"><span class="s1" style="color: #d14;">* when all samples appear in the same order as they do in the .fam file,</span></span>
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1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="mosel"><span class="s1" style="color: #d14;">you can use the '</span><span class="n" style="color: #333;">noheader</span><span class="s1" style="color: #d14;">' modifier.</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Otherwise, use the '</span><span class="n" style="color: #333;">sepheader</span><span class="s1" style="color: #d14;">' modifier, and append sample ID filenames</span></span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="mosel"><span class="s1" style="color: #d14;">to your '</span><span class="k" style="font-weight: 600;">list</span><span class="s1" style="color: #d14;">' file entries.</span></span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The '</span><span class="n" style="color: #333;">format</span><span class="p">=</span><span class="s1" style="color: #d14;">' modifier lets you specify the number of values used to</span></span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="mosel"><span class="s1" style="color: #d14;">represent each dosage.</span></span>
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1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">format</span><span class="p">=</span><span class="m" style="color: #099;">1</span><span class="s1" style="color: #d14;">' normally indicates a single 0..2 A1</span></span>
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1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="mosel"><span class="s1" style="color: #d14;">expected count; '</span><span class="n" style="color: #333;">dose1</span><span class="s1" style="color: #d14;">' modifies this to a 0..1 frequency.</span></span>
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1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">format</span><span class="p">=</span><span class="m" style="color: #099;">2</span><span class="s1" style="color: #d14;">'</span></span>
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1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="mosel"><span class="s1" style="color: #d14;">(the default) indicates a 0..1 homozygous A1 likelihood followed by a</span></span>
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1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="mosel"><span class="s1" style="color: #d14;">0..1 het likelihood, while '</span><span class="n" style="color: #333;">format</span><span class="p">=</span><span class="m" style="color: #099;">3</span><span class="s1" style="color: #d14;">' indicates 0..1 hom A1, 0..1 het,</span></span>
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1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="mosel"><span class="s1" style="color: #d14;">0..1 hom A2.</span></span>
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1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">Zout</span><span class="s1" style="color: #d14;">' causes the output file to be gzipped.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Normally, an association analysis is performed. '</span><span class="n" style="color: #333;">standard</span><span class="p">\-</span><span class="n" style="color: #333;">beta</span><span class="s1" style="color: #d14;">' and</span></span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">sex</span><span class="s1" style="color: #d14;">' behave as they are supposed to with \fB\-\-linear\fR/\-\-logistic.</span></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="k" style="font-weight: 600;">case</span><span class="p">\-</span><span class="n" style="color: #333;">control</span><span class="p">\-</span><span class="n" style="color: #333;">freqs</span><span class="s1" style="color: #d14;">' causes case and control allele frequencies to be</span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="mosel"><span class="s1" style="color: #d14;">reported separately.</span></span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="mosel"><span class="s1" style="color: #d14;">* There are three alternate modes which cause the association analysis to</span></span>
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1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="mosel"><span class="s1" style="color: #d14;">be skipped.</span></span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">occur</span><span class="s1" style="color: #d14;">' requests a simple variant occurrence report.</span></span>
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1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="mosel"><span class="s1" style="color: #d14;">* \fB\-\-write\-dosage\fR causes a simple merged file matching the '</span><span class="n" style="color: #333;">format</span><span class="s1" style="color: #d14;">'</span></span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="mosel"><span class="s1" style="color: #d14;">specification (not including '</span><span class="n" style="color: #333;">dose1</span><span class="s1" style="color: #d14;">') to be generated.</span></span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="mosel"><span class="s1" style="color: #d14;">* \fB\-\-score\fR applies a linear scoring system to the dosages.</span></span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-lasso\fR <h2 estimate> [min lambda] ['</span><span class="n" style="color: #333;">report</span><span class="p">\-</span><span class="n" style="color: #333;">zeroes</span><span class="s1" style="color: #d14;">']</span></span>
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1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="mosel"><span class="s1" style="color: #d14;">Estimate variant effect sizes via LASSO regression.</span></span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="mosel"><span class="s1" style="color: #d14;">You must provide an</span></span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="mosel"><span class="s1" style="color: #d14;">additive heritability estimate to calibrate the regression.</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="mosel"><span class="s1" style="color: #d14;">Note that this method may require a very large sample size (e.g. hundreds</span></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="mosel"><span class="s1" style="color: #d14;">of thousands) to be effective on complex polygenic traits.</span></span>
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1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-test\-missing\fR ['</span><span class="n" style="color: #333;">perm</span><span class="s1" style="color: #d14;">' | '</span><span class="n" style="color: #333;">mperm</span><span class="p">=</span><span class="s1" style="color: #d14;">'<value>] ['</span><span class="n" style="color: #333;">perm</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">midp</span><span class="s1" style="color: #d14;">']</span></span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="mosel"><span class="s1" style="color: #d14;">Check for association between missingness and case/control status, using</span></span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="mosel"><span class="s1" style="color: #d14;">Fisher'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">exact</span> <span class="n" style="color: #333;">test</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Het</span><span class="p">.</span> <span class="n" style="color: #333;">haploids</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">treated</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">missing</span><span class="p">.)</span></span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'midp'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">Lancaster</span><span class="s1" style="color: #d14;">'s mid\-p adjustment to be applied.</span></span>
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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-make\-perm\-pheno\fR <ct></span></span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="mosel"><span class="s1" style="color: #d14;">Generate phenotype permutations and write them to disk, without invoking an</span></span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="mosel"><span class="s1" style="color: #d14;">association test.</span></span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tdt\fR [{exact | exact\-midp | poo}] ['</span><span class="n" style="color: #333;">perm</span><span class="s1" style="color: #d14;">' | '</span><span class="n" style="color: #333;">mperm</span><span class="p">=</span><span class="s1" style="color: #d14;">'<value>] ['</span><span class="n" style="color: #333;">perm</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="s1" style="color: #d14;">']</span></span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="mosel"><span class="s1" style="color: #d14;">[{parentdt1 | parentdt2 | pat | mat}] ['</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">test</span><span class="s1" style="color: #d14;">']</span></span>
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1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="mosel"><span class="s1" style="color: #d14;">Report transmission disequilibrium test statistics, given case/control</span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="mosel"><span class="s1" style="color: #d14;">phenotypes and pedigree information.</span></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="mosel"><span class="s1" style="color: #d14;">* A Mendel error check is performed before the main tests; offending</span></span>
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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="mosel"><span class="s1" style="color: #d14;">genotypes are treated as missing by this analysis.</span></span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="mosel"><span class="s1" style="color: #d14;">* By default, the basic TDT p\-value is based on a chi\-square test unless</span></span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="mosel"><span class="s1" style="color: #d14;">you request the exact binomial test with '</span><span class="n" style="color: #333;">exact</span><span class="s1" style="color: #d14;">' or '</span><span class="n" style="color: #333;">exact</span><span class="p">\-</span><span class="n" style="color: #333;">midp</span><span class="s1" style="color: #d14;">'.</span></span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">perm</span><span class="s1" style="color: #d14;">'/'</span><span class="n" style="color: #333;">mperm</span><span class="p">=</span><span class="s1" style="color: #d14;">' requests a family\-based adaptive or max(T) permutation</span></span>
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1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="mosel"><span class="s1" style="color: #d14;">test.</span></span>
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1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="mosel"><span class="s1" style="color: #d14;">By default, the permutation test statistic is the basic TDT</span></span>
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1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="mosel"><span class="s1" style="color: #d14;">p\-value; '</span><span class="n" style="color: #333;">parentdt1</span><span class="s1" style="color: #d14;">'/'</span><span class="n" style="color: #333;">parentdt2</span><span class="s1" style="color: #d14;">' cause parenTDT or combined test</span></span>
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1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="mosel"><span class="s1" style="color: #d14;">p\-values, respectively, to be considered instead.</span></span>
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1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">test</span><span class="s1" style="color: #d14;">' tests the significance of variant sets.</span></span>
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1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="mosel"><span class="s1" style="color: #d14;">This cannot be used</span></span>
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1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1202
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="mosel"><span class="s1" style="color: #d14;">with exact tests for now.</span></span>
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1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="mosel"><span class="s1" style="color: #d14;">The '</span><span class="n" style="color: #333;">poo</span><span class="s1" style="color: #d14;">' modifier causes a parent\-of\-origin analysis to be performed</span></span>
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1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="mosel"><span class="s1" style="color: #d14;">instead, with transmissions from heterozygous fathers and heterozygous</span></span>
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1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="mosel"><span class="s1" style="color: #d14;">mothers considered separately.</span></span>
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1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The parent\-of\-origin analysis does not currently support exact tests.</span></span>
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1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="mosel"><span class="s1" style="color: #d14;">* By default, the permutation test statistic is the absolute</span></span>
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1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="mosel"><span class="s1" style="color: #d14;">parent\-of\-origin test Z score; '</span><span class="n" style="color: #333;">pat</span><span class="s1" style="color: #d14;">'/'</span><span class="n" style="color: #333;">mat</span><span class="s1" style="color: #d14;">' cause paternal or maternal TDT</span></span>
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1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="mosel"><span class="s1" style="color: #d14;">chi\-square statistics, respectively, to be considered instead.</span></span>
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1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-qfam\fR ['</span><span class="n" style="color: #333;">perm</span><span class="s1" style="color: #d14;">' | '</span><span class="n" style="color: #333;">mperm</span><span class="p">=</span><span class="s1" style="color: #d14;">'<value>] ['</span><span class="n" style="color: #333;">perm</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">emp</span><span class="p">\-</span><span class="n" style="color: #333;">se</span><span class="s1" style="color: #d14;">']</span></span>
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1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-qfam\-parents\fR ['</span><span class="n" style="color: #333;">perm</span><span class="s1" style="color: #d14;">' | '</span><span class="n" style="color: #333;">mperm</span><span class="p">=</span><span class="s1" style="color: #d14;">'<value>] ['</span><span class="n" style="color: #333;">perm</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">emp</span><span class="p">\-</span><span class="n" style="color: #333;">se</span><span class="s1" style="color: #d14;">']</span></span>
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1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1217
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-qfam\-between\fR ['</span><span class="n" style="color: #333;">perm</span><span class="s1" style="color: #d14;">' | '</span><span class="n" style="color: #333;">mperm</span><span class="p">=</span><span class="s1" style="color: #d14;">'<value>] ['</span><span class="n" style="color: #333;">perm</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">emp</span><span class="p">\-</span><span class="n" style="color: #333;">se</span><span class="s1" style="color: #d14;">']</span></span>
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1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-qfam\-total\fR ['</span><span class="n" style="color: #333;">perm</span><span class="s1" style="color: #d14;">' | '</span><span class="n" style="color: #333;">mperm</span><span class="p">=</span><span class="s1" style="color: #d14;">'<value>] ['</span><span class="n" style="color: #333;">perm</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">emp</span><span class="p">\-</span><span class="n" style="color: #333;">se</span><span class="s1" style="color: #d14;">']</span></span>
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1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="mosel"><span class="s1" style="color: #d14;">QFAM family\-based association test for quantitative traits.</span></span>
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1222
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="mosel"><span class="s1" style="color: #d14;">* A Mendel error check is performed before the main tests; offending</span></span>
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1223
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1224
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="mosel"><span class="s1" style="color: #d14;">genotypes are treated as missing by this analysis.</span></span>
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1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="mosel"><span class="s1" style="color: #d14;">* This procedure requires permutation.</span></span>
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1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">perm</span><span class="s1" style="color: #d14;">' and '</span><span class="n" style="color: #333;">perm</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="s1" style="color: #d14;">' have the</span></span>
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1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="mosel"><span class="s1" style="color: #d14;">usual meanings.</span></span>
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1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="mosel"><span class="s1" style="color: #d14;">However, '</span><span class="n" style="color: #333;">mperm</span><span class="p">=</span><span class="s1" style="color: #d14;">'<value> just specifies a fixed number</span></span>
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1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="mosel"><span class="s1" style="color: #d14;">of permutations; the method does not support a proper max(T) test.</span></span>
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1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The '</span><span class="n" style="color: #333;">emp</span><span class="p">\-</span><span class="n" style="color: #333;">se</span><span class="s1" style="color: #d14;">' modifier adds BETA and EMP_SE (empirical standard error for</span></span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="mosel"><span class="s1" style="color: #d14;">beta) fields to the .perm output file.</span></span>
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1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-annotate\fR <PLINK report> ['</span><span class="n" style="color: #333;">attrib</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file>] ['</span><span class="n" style="color: #333;">ranges</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file>]</span></span>
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1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="mosel"><span class="s1" style="color: #d14;">['</span><span class="n" style="color: #333;">filter</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file>] ['</span><span class="n" style="color: #333;">snps</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file>] [{NA | prune}] ['</span><span class="n" style="color: #333;">block</span><span class="s1" style="color: #d14;">']</span></span>
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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="mosel"><span class="s1" style="color: #d14;">['</span><span class="n" style="color: #333;">subset</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file>] ['</span><span class="n" style="color: #333;">minimal</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">distance</span><span class="s1" style="color: #d14;">']</span></span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="mosel"><span class="s1" style="color: #d14;">Add annotations to a variant\-based PLINK report.</span></span>
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1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="mosel"><span class="s1" style="color: #d14;">This requires an</span></span>
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1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="mosel"><span class="s1" style="color: #d14;">annotation source:</span></span>
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1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">attrib</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file> specifies a (possibly gzipped) attribute file.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">ranges</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file> specifies a gene/range list file.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="mosel"><span class="s1" style="color: #d14;">(Both source types can be specified simultaneously.) The following options</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="mosel"><span class="s1" style="color: #d14;">are also supported:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">filter</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file> causes only variants within one of the ranges in the file</span></span>
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1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="mosel"><span class="s1" style="color: #d14;">to be included in the new report.</span></span>
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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="mosel"><span class="s1" style="color: #d14;">* '</span><span class="n" style="color: #333;">snps</span><span class="p">=</span><span class="s1" style="color: #d14;">'<file> causes only variants named in the file to be included in</span></span>
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1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="mosel"><span class="s1" style="color: #d14;">the new report.</span></span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The '</span><span class="n" style="color: #333;">NA</span><span class="s1" style="color: #d14;">' modifier causes unannotated variants to have '</span><span class="n" style="color: #333;">NA</span><span class="s1" style="color: #d14;">' instead of '</span><span class="p">.</span><span class="s1" style="color: #d14;">'</span></span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="mosel"><span class="s1" style="color: #d14;">in the new report'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">ANNOT</span> <span class="n" style="color: #333;">column</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'prune'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">excludes</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="mosel"><span class="n" style="color: #333;">them</span> <span class="n" style="color: #333;">entirely</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'block'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">replaces</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">ANNOT</span> <span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="m" style="color: #099;">0</span><span class="p">/</span><span class="m" style="color: #099;">1</span><span class="p">\-</span><span class="n" style="color: #333;">coded</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="mosel"><span class="n" style="color: #333;">column</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">possible</span> <span class="n" style="color: #333;">annotation</span><span class="p">.</span></span>
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1267
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">With</span> <span class="s1" style="color: #d14;">'ranges'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'subset='</span><span class="p"><</span><span class="n" style="color: #333;">file</span><span class="p">></span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">intervals</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">subset</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="mosel"><span class="n" style="color: #333;">loaded</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">ranges</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">interval</span> <span class="n" style="color: #333;">annotations</span> <span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">come</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">parenthesized</span> <span class="n" style="color: #333;">signed</span> <span class="n" style="color: #333;">distance</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">interval</span> <span class="n" style="color: #333;">boundary</span> <span class="p">(</span><span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">located</span> <span class="n" style="color: #333;">inside</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="mosel"><span class="n" style="color: #333;">interval</span><span class="p">;</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">always</span> <span class="nb" style="color: #0086b3;">true</span> <span class="n" style="color: #333;">without</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">border</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">).</span> <span class="n" style="color: #333;">They</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">excluded</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="mosel"><span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'minimal'</span> <span class="n" style="color: #333;">modifier</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'distance'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">adds</span> <span class="s1" style="color: #d14;">'DIST'</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'SGN'</span> <span class="n" style="color: #333;">columns</span> <span class="n" style="color: #333;">describing</span> <span class="n" style="color: #333;">signed</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="mosel"><span class="n" style="color: #333;">distance</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">nearest</span> <span class="n" style="color: #333;">interval</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">When</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pfilter</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">present</span><span class="p">,</span> <span class="n" style="color: #333;">high</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">filtered</span> <span class="n" style="color: #333;">out</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">filename</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="mosel"><span class="n" style="color: #333;">Process</span> <span class="n" style="color: #333;">association</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">report</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">with</span> <span class="s1" style="color: #d14;">'SNP'</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">columns</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="mosel"><span class="n" style="color: #333;">organizing</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">LD</span><span class="p">\-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">clumps</span><span class="p">.</span> <span class="n" style="color: #333;">Multiple</span> <span class="n" style="color: #333;">filenames</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">separated</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="mosel"><span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">spaces</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">commas</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="n" style="color: #333;">report</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">report</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">gene</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">file</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="mosel"><span class="n" style="color: #333;">Generate</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">report</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variant</span><span class="p">\-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">When</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pfilter</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">present</span><span class="p">,</span> <span class="n" style="color: #333;">high</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">filtered</span> <span class="n" style="color: #333;">out</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">When</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">extract</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">(</span><span class="n" style="color: #333;">without</span> <span class="s1" style="color: #d14;">'range'</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">present</span><span class="p">,</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1297
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">extract</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">considered</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1299
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">filenames</span><span class="p">...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">filenames</span><span class="p">...></span> <span class="p">+</span> <span class="p">[{</span><span class="n" style="color: #333;">logscale</span> <span class="p">|</span> <span class="n" style="color: #333;">qt</span><span class="p">}]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">map</span> <span class="p">|</span> <span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">allele</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'study'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'report\-all'</span><span class="p">]</span></span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="mosel"><span class="p">[</span><span class="s1" style="color: #d14;">'weighted\-z'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="mosel"><span class="n" style="color: #333;">Perform</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">several</span> <span class="n" style="color: #333;">variant</span><span class="p">\-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">reports</span> <span class="k" style="font-weight: 600;">with</span> <span class="s1" style="color: #d14;">'SNP'</span> <span class="k" style="font-weight: 600;">and</span></span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'SE'</span> <span class="n" style="color: #333;">fields</span><span class="p">.</span></span>
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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Normally</span><span class="p">,</span> <span class="n" style="color: #333;">an</span> <span class="s1" style="color: #d14;">'OR'</span> <span class="n" style="color: #333;">odds</span> <span class="n" style="color: #333;">ratio</span> <span class="n" style="color: #333;">field</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">present</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">input</span></span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="mosel"><span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="mosel"><span class="k" style="font-weight: 600;">With</span> <span class="s1" style="color: #d14;">'logscale'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'BETA'</span> <span class="nb" style="color: #0086b3;">log</span><span class="p">\-</span><span class="n" style="color: #333;">odds</span> <span class="n" style="color: #333;">values</span><span class="p">/</span><span class="n" style="color: #333;">regression</span> <span class="n" style="color: #333;">coefficients</span></span>
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1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">expected</span> <span class="n" style="color: #333;">instead</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">generated</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">odds</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="mosel"><span class="n" style="color: #333;">ratio</span> <span class="n" style="color: #333;">estimates</span><span class="p">.</span> <span class="k" style="font-weight: 600;">With</span> <span class="s1" style="color: #d14;">'qt'</span><span class="p">,</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">input</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">regression</span></span>
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1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="mosel"><span class="n" style="color: #333;">betas</span><span class="p">.</span></span>
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1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'CHR'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'BP'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'A1'</span> <span class="n" style="color: #333;">fields</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">required</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'no\-map'</span> <span class="n" style="color: #333;">causes</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="mosel"><span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">ignored</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="s1" style="color: #d14;">'no\-allele'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">just</span> <span class="s1" style="color: #d14;">'A1'</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">ignored</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="mosel"><span class="p">*</span> <span class="k" style="font-weight: 600;">If</span> <span class="s1" style="color: #d14;">'A2'</span> <span class="n" style="color: #333;">fields</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">neither</span> <span class="s1" style="color: #d14;">'no\-map'</span> <span class="n" style="color: #333;">nor</span> <span class="s1" style="color: #d14;">'no\-allele'</span> <span class="n" style="color: #333;">was</span></span>
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1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span><span class="p">,</span> <span class="n" style="color: #333;">A1</span><span class="p">/</span><span class="n" style="color: #333;">A2</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">flips</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">handled</span> <span class="n" style="color: #333;">properly</span><span class="p">.</span></span>
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1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="mosel"><span class="n" style="color: #333;">Otherwise</span><span class="p">,</span> <span class="n" style="color: #333;">A1</span></span>
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1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="mosel"><span class="n" style="color: #333;">mismatches</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">thrown</span> <span class="n" style="color: #333;">out</span><span class="p">.</span></span>
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1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'study'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">study</span><span class="p">\-</span><span class="n" style="color: #333;">specific</span> <span class="n" style="color: #333;">effect</span> <span class="n" style="color: #333;">estimates</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">collated</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="mosel"><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'report\-all'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">present</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span></span>
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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="mosel"><span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'weighted\-z'</span> <span class="n" style="color: #333;">requests</span> <span class="n" style="color: #333;">weighted</span> <span class="n" style="color: #333;">Z</span><span class="p">\-</span><span class="n" style="color: #333;">score</span><span class="p">\-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">values</span> <span class="p">(</span><span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">computed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span></span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="mosel"><span class="n" style="color: #333;">Abecasis</span> <span class="n" style="color: #333;">Lab</span><span class="s1" style="color: #d14;">'s METAL software) in addition to the usual inverse</span></span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="mosel"><span class="s1" style="color: #d14;">variance\-based analysis. This requires P and effective sample size</span></span>
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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="mosel"><span class="s1" style="color: #d14;">fields.</span></span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="mosel"><span class="s1" style="color: #d14;">* When \fB\-\-extract\fR (without '</span><span class="k" style="font-weight: 600;">range</span><span class="s1" style="color: #d14;">') is present, only variants named in the</span></span>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-extract\fR file are considered.</span></span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Unless '</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">map</span><span class="s1" style="color: #d14;">' is specified, chromosome filters are also respected.</span></span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-fast\-epistasis\fR [{boost | joint\-effects | no\-ueki}] ['</span><span class="k" style="font-weight: 600;">case</span><span class="p">\-</span><span class="n" style="color: #333;">only</span><span class="s1" style="color: #d14;">']</span></span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="mosel"><span class="s1" style="color: #d14;">[{set\-by\-set | set\-by\-all}] ['</span><span class="n" style="color: #333;">nop</span><span class="s1" style="color: #d14;">']</span></span>
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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-epistasis\fR [{set\-by\-set | set\-by\-all}]</span></span>
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1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1356
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="mosel"><span class="s1" style="color: #d14;">Scan for epistatic interactions.</span></span>
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1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-fast\-epistasis\fR inspects 3x3 joint</span></span>
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1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="mosel"><span class="s1" style="color: #d14;">genotype count tables and only applies to case/control phenotypes, while</span></span>
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1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-epistasis\fR performs linear or logistic regression.</span></span>
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1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="mosel"><span class="s1" style="color: #d14;">* By default, \fB\-\-fast\-epistasis\fR uses the PLINK 1.07 allele\-based test. Two</span></span>
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1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="mosel"><span class="s1" style="color: #d14;">newer tests are now supported: '</span><span class="n" style="color: #333;">boost</span><span class="s1" style="color: #d14;">' invokes the likelihood ratio test</span></span>
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1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="mosel"><span class="s1" style="color: #d14;">introduced by Wan X et al. (2010) BOOST: A Fast Approach to Detecting</span></span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="mosel"><span class="s1" style="color: #d14;">Gene\-Gene Interactions in Genome\-wide Case\-Control Studies, while</span></span>
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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="mosel"><span class="s1" style="color: #d14;">\&'</span><span class="n" style="color: #333;">joint</span><span class="p">\-</span><span class="n" style="color: #333;">effects</span><span class="s1" style="color: #d14;">' applies the joint effects test introduced in Ueki M,</span></span>
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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="mosel"><span class="s1" style="color: #d14;">Cordell HJ (2012) Improved statistics for genome\-wide interaction</span></span>
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1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="mosel"><span class="s1" style="color: #d14;">analysis.</span></span>
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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The original \fB\-\-fast\-epistasis\fR test normally applies the variance and</span></span>
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1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="mosel"><span class="s1" style="color: #d14;">empty cell corrections suggested by Ueki and Cordell'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">paper</span><span class="p">.</span></span>
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1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="mosel"><span class="k" style="font-weight: 600;">To</span> <span class="n" style="color: #333;">disable</span></span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="mosel"><span class="n" style="color: #333;">them</span><span class="p">,</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'no\-ueki'</span> <span class="n" style="color: #333;">modifier</span><span class="p">.</span></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'case\-only'</span> <span class="n" style="color: #333;">requests</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">case</span><span class="p">\-</span><span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">test</span><span class="p">.</span></span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">pairs</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">across</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">entire</span> <span class="n" style="color: #333;">genome</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">tested</span><span class="p">.</span></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1380
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<pre style="margin: 0;">+<span id="LC1380" class="line" lang="mosel"><span class="k" style="font-weight: 600;">To</span> <span class="n" style="color: #333;">just</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">pairs</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">within</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span> <span class="k" style="font-weight: 600;">set</span><span class="p">,</span> <span class="n" style="color: #333;">add</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'set\-by\-set'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1381
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<pre style="margin: 0;">+<span id="LC1381" class="line" lang="mosel"><span class="n" style="color: #333;">modifier</span> <span class="k" style="font-weight: 600;">and</span> <span class="nf" style="color: #900; font-weight: 600;">load</span> <span class="n" style="color: #333;">exactly</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">;</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">exactly</span> <span class="n" style="color: #333;">two</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1382
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="mosel"><span class="n" style="color: #333;">sets</span> <span class="n" style="color: #333;">loaded</span><span class="p">,</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">against</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">other</span><span class="p">.</span> <span class="s1" style="color: #d14;">'set\-by\-all'</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">against</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">entire</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="mosel"><span class="n" style="color: #333;">genome</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span></span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1386
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<pre style="margin: 0;">+<span id="LC1386" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'nop'</span> <span class="n" style="color: #333;">strips</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">values</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">main</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1387
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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">computations</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">subdivided</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">parallel</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">;</span> <span class="n" style="color: #333;">however</span><span class="p">...</span></span>
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1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1389
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">epistasis</span><span class="p">\-</span><span class="n" style="color: #333;">summary</span><span class="p">\-</span><span class="n" style="color: #333;">merge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">common</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">prefix</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">ct</span><span class="p">></span></span>
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1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="mosel"><span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">a</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-[</span><span class="n" style="color: #333;">fast</span><span class="p">\-]</span><span class="n" style="color: #333;">epistasis</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">job</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">subdivided</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">parallel</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">main</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="mosel"><span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">assembled</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">applying</span> <span class="n" style="color: #333;">Unix</span> <span class="s1" style="color: #d14;">'cat'</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">usual</span></span>
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1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="mosel"><span class="n" style="color: #333;">manner</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">the</span> <span class="p">.</span><span class="n" style="color: #333;">summary</span><span class="m" style="color: #099;">.1</span><span class="p">,</span> <span class="p">.</span><span class="n" style="color: #333;">summary</span><span class="m" style="color: #099;">.2</span><span class="p">,</span> <span class="p">...</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">require</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">specialized</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="mosel"><span class="n" style="color: #333;">merge</span><span class="p">.</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">epistasis</span><span class="p">\-</span><span class="n" style="color: #333;">summary</span><span class="p">\-</span><span class="n" style="color: #333;">merge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">takes</span> <span class="n" style="color: #333;">care</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">latter</span><span class="p">.</span></span>
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1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">twolocus</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ID</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ID</span><span class="p">></span></span>
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1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="mosel"><span class="n" style="color: #333;">Two</span><span class="p">\-</span><span class="n" style="color: #333;">locus</span> <span class="n" style="color: #333;">joint</span> <span class="n" style="color: #333;">genotype</span> <span class="k" style="font-weight: 600;">count</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">score</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'header'</span><span class="p">]</span> <span class="p">[{</span><span class="k" style="font-weight: 600;">sum</span> <span class="p">|</span> <span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="k" style="font-weight: 600;">sum</span><span class="p">}]</span></span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="mosel"><span class="p">[{</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">mean</span><span class="p">\-</span><span class="n" style="color: #333;">imputation</span> <span class="p">|</span> <span class="n" style="color: #333;">center</span><span class="p">}]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'include\-cnt'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'double\-dosage'</span><span class="p">]</span></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="mosel"><span class="n" style="color: #333;">Apply</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">linear</span> <span class="n" style="color: #333;">scoring</span> <span class="nf" style="color: #900; font-weight: 600;">system</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">per</span> <span class="n" style="color: #333;">scored</span> <span class="n" style="color: #333;">variant</span><span class="p">.</span> <span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">IDs</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="mosel"><span class="nb" style="color: #0086b3;">read</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">column</span> <span class="p">#</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">codes</span> <span class="n" style="color: #333;">are</span> <span class="nb" style="color: #0086b3;">read</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">column</span> <span class="p">#</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">scores</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="mosel"><span class="nb" style="color: #0086b3;">read</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">column</span> <span class="p">#</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">i</span> <span class="n" style="color: #333;">defaults</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">j</span> <span class="n" style="color: #333;">defaults</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">i</span><span class="p">+</span><span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">k</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="mosel"><span class="n" style="color: #333;">defaults</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">j</span><span class="p">+</span><span class="m" style="color: #099;">1.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'header'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">nonempty</span> <span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="mosel"><span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">ignored</span><span class="p">;</span> <span class="n" style="color: #333;">otherwise</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">score</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">assumes</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">header</span> <span class="n" style="color: #333;">line</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">final</span> <span class="n" style="color: #333;">scores</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">averages</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">valid</span> <span class="n" style="color: #333;">per</span><span class="p">\-</span><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">scores</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1414
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1415
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'sum'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">sums</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">reported</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="mosel"><span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="s1" style="color: #d14;">'no\-mean\-imputation'</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1419
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<pre style="margin: 0;">+<span id="LC1419" class="line" lang="mosel"><span class="k" style="font-weight: 600;">And</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">backward</span> <span class="n" style="color: #333;">compatibility</span><span class="p">,</span> <span class="s1" style="color: #d14;">'sum'</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="mosel"><span class="n" style="color: #333;">automatically</span> <span class="n" style="color: #333;">on</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dosage</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">unless</span> <span class="s1" style="color: #d14;">'no\-sum'</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">specified</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">copies</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">unnamed</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">contribute</span> <span class="n" style="color: #333;">zero</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span></span>
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1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="mosel"><span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">genotypes</span> <span class="n" style="color: #333;">contribute</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">amount</span> <span class="n" style="color: #333;">proportional</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">loaded</span> <span class="p">(</span><span class="n" style="color: #333;">via</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">read</span><span class="p">\-</span><span class="n" style="color: #333;">freq</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">imputed</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">frequency</span><span class="p">.</span> <span class="k" style="font-weight: 600;">To</span> <span class="n" style="color: #333;">throw</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">missing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="mosel"><span class="n" style="color: #333;">observations</span> <span class="n" style="color: #333;">instead</span> <span class="p">(</span><span class="n" style="color: #333;">decreasing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">denominator</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">final</span> <span class="n" style="color: #333;">average</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1428
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<pre style="margin: 0;">+<span id="LC1428" class="line" lang="mosel"><span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">happens</span><span class="p">),</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'no\-mean\-imputation'</span> <span class="n" style="color: #333;">modifier</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1429
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<pre style="margin: 0;">+<span id="LC1429" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Alternatively</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'center'</span> <span class="n" style="color: #333;">modifier</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">shift</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">scores</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="mosel"><span class="n" style="color: #333;">mean</span> <span class="n" style="color: #333;">zero</span><span class="p">.</span></span>
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1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">This</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dosage</span> <span class="n" style="color: #333;">data</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1435
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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="mosel"><span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'CNT'</span> <span class="n" style="color: #333;">column</span></span>
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1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">omitted</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">case</span><span class="p">;</span> <span class="n" style="color: #333;">use</span> <span class="s1" style="color: #d14;">'include\-cnt'</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">keep</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="mosel"><span class="n" style="color: #333;">it</span><span class="p">.</span> <span class="n" style="color: #333;">Also</span><span class="p">,</span> <span class="n" style="color: #333;">note</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">scores</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">multiplied</span> <span class="n" style="color: #333;">by</span> <span class="m" style="color: #099;">0..1</span> <span class="n" style="color: #333;">dosages</span><span class="p">,</span> <span class="k" style="font-weight: 600;">not</span> <span class="m" style="color: #099;">0..2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="mosel"><span class="n" style="color: #333;">diploid</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="n" style="color: #333;">unless</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'double\-dosage'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">present</span><span class="p">.</span></span>
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1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">R</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">R</span> <span class="n" style="color: #333;">script</span> <span class="n" style="color: #333;">file</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'debug'</span><span class="p">]</span></span>
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1442
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<pre style="margin: 0;">+<span id="LC1442" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="mosel"><span class="nf" style="color: #900; font-weight: 600;">Connect</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Rserve</span> <span class="p">(</span><span class="n" style="color: #333;">preferably</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">1.7</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">later</span><span class="p">)</span> <span class="n" style="color: #333;">background</span> <span class="n" style="color: #333;">process</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1444
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<pre style="margin: 0;">+<span id="LC1444" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">execute</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Rplink</span> <span class="k" style="font-weight: 600;">function</span> <span class="n" style="color: #333;">defined</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">file</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Unless</span> <span class="n" style="color: #333;">the</span></span>
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1445
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'debug'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">present</span><span class="p">;</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">case</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">R</span> <span class="n" style="color: #333;">commands</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">would</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="mosel"><span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">tried</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">execute</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">logged</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">file</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1447
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<pre style="margin: 0;">+<span id="LC1447" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1448
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<pre style="margin: 0;">+<span id="LC1448" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">var</span><span class="p">\-</span><span class="n" style="color: #333;">ranges</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">block</span> <span class="n" style="color: #333;">ct</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1449
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1450
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<pre style="margin: 0;">+<span id="LC1450" class="line" lang="mosel"><span class="n" style="color: #333;">Divide</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">equal</span><span class="p">\-</span><span class="n" style="color: #333;">size</span> <span class="n" style="color: #333;">blocks</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1451
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<pre style="margin: 0;">+<span id="LC1451" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">Can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1453
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<pre style="margin: 0;">+<span id="LC1453" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">snps</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">split</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">job</span> <span class="n" style="color: #333;">across</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">machines</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1454
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">PP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1455
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">flags</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">supported</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Order</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">operations</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">described</span> <span class="n" style="color: #333;">at</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">cog</span><span class="p">\-</span><span class="n" style="color: #333;">genomics</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">plink</span><span class="p">/</span><span class="m" style="color: #099;">1.9</span><span class="p">/</span><span class="n" style="color: #333;">order</span> <span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1458
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<pre style="margin: 0;">+<span id="LC1458" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">script</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">fname</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="nf" style="color: #900; font-weight: 600;">command</span><span class="p">\-</span><span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">options</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1459
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<pre style="margin: 0;">+<span id="LC1459" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1460
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<pre style="margin: 0;">+<span id="LC1460" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">rerun</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">log</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Rerun</span> <span class="n" style="color: #333;">commands</span> <span class="k" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">log</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="s1" style="color: #d14;">'plink.log'</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1462
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<pre style="margin: 0;">+<span id="LC1462" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">version</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1464
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Display</span> <span class="n" style="color: #333;">only</span> <span class="k" style="font-weight: 600;">version</span> <span class="n" style="color: #333;">number</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">exiting</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1465
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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1466
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<pre style="margin: 0;">+<span id="LC1466" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">silent</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1467
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<pre style="margin: 0;">+<span id="LC1467" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Suppress</span> <span class="n" style="color: #333;">output</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">console</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1468
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<pre style="margin: 0;">+<span id="LC1468" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1469
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<pre style="margin: 0;">+<span id="LC1469" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gplink</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1470
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<pre style="margin: 0;">+<span id="LC1470" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Reserved</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">interoperation</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">gPLINK</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1471
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<pre style="margin: 0;">+<span id="LC1471" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1472
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<pre style="margin: 0;">+<span id="LC1472" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">genotype</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">char</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">code</span> <span class="p">(</span><span class="n" style="color: #333;">normally</span> <span class="s1" style="color: #d14;">'0'</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1473
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<pre style="margin: 0;">+<span id="LC1473" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1474
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<pre style="margin: 0;">+<span id="LC1474" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">double</span><span class="p">\-</span><span class="n" style="color: #333;">id</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1475
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<pre style="margin: 0;">+<span id="LC1475" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">FIDs</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">IIDs</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">VCF</span><span class="p">/</span><span class="n" style="color: #333;">BCF</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">ID</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1477
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<pre style="margin: 0;">+<span id="LC1477" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">const</span><span class="p">\-</span><span class="n" style="color: #333;">fid</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">ID</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1478
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<pre style="margin: 0;">+<span id="LC1478" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">FIDs</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">constant</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="s1" style="color: #d14;">'0'</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1479
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<pre style="margin: 0;">+<span id="LC1479" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1480
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">id</span><span class="p">\-</span><span class="n" style="color: #333;">delim</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">d</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1481
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<pre style="margin: 0;">+<span id="LC1481" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Parse</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">as</span> <span class="p"><</span><span class="n" style="color: #333;">FID</span><span class="p">><</span><span class="n" style="color: #333;">d</span><span class="p">><</span><span class="n" style="color: #333;">IID</span><span class="p">></span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">delim</span> <span class="s1" style="color: #d14;">'_'</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1483
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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="n" style="color: #333;">idspace</span><span class="p">\-</span><span class="k" style="font-weight: 600;">to</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">c</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Convert</span> <span class="n" style="color: #333;">spaces</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">character</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1484
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<pre style="margin: 0;">+<span id="LC1484" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1485
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<pre style="margin: 0;">+<span id="LC1485" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">biallelic</span><span class="p">\-</span><span class="n" style="color: #333;">only</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'strict'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'list'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Skip</span> <span class="n" style="color: #333;">VCF</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="m" style="color: #099;">2</span><span class="p">+</span> <span class="n" style="color: #333;">ALT</span> <span class="n" style="color: #333;">alleles</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1486
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<pre style="margin: 0;">+<span id="LC1486" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1487
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<pre style="margin: 0;">+<span id="LC1487" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="k" style="font-weight: 600;">min</span><span class="p">\-</span><span class="n" style="color: #333;">qual</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1488
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<pre style="margin: 0;">+<span id="LC1488" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Skip</span> <span class="n" style="color: #333;">VCF</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">low</span><span class="p">/</span><span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">QUAL</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1489
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<pre style="margin: 0;">+<span id="LC1489" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1490
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<pre style="margin: 0;">+<span id="LC1490" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="n" style="color: #333;">filter</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">exception</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...]</span> <span class="p">:</span> <span class="n" style="color: #333;">Skip</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">FILTER</span> <span class="n" style="color: #333;">failures</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1491
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<pre style="margin: 0;">+<span id="LC1491" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1492
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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="n" style="color: #333;">require</span><span class="p">\-</span><span class="n" style="color: #333;">gt</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1493
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<pre style="margin: 0;">+<span id="LC1493" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Skip</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">field</span><span class="p">.</span></span>
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1494
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<pre style="margin: 0;">+<span id="LC1494" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1495
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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="k" style="font-weight: 600;">min</span><span class="p">\-</span><span class="n" style="color: #333;">gq</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1496
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<pre style="margin: 0;">+<span id="LC1496" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">No</span><span class="p">\-</span><span class="n" style="color: #333;">call</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">GQ</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">below</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1497
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="mosel"><span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">threshold</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1498
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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="k" style="font-weight: 600;">min</span><span class="p">\-</span><span class="n" style="color: #333;">gp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1500
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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">No</span><span class="p">\-</span><span class="n" style="color: #333;">call</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">when</span> <span class="m" style="color: #099;">0</span><span class="p">\-</span><span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">scaled</span> <span class="n" style="color: #333;">GP</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1501
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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="mosel"><span class="n" style="color: #333;">below</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">threshold</span><span class="p">.</span></span>
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1502
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<pre style="margin: 0;">+<span id="LC1502" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1503
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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">vcf</span><span class="p">\-</span><span class="n" style="color: #333;">half</span><span class="p">\-</span><span class="n" style="color: #333;">call</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">m</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1504
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<pre style="margin: 0;">+<span id="LC1504" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">how</span> <span class="s1" style="color: #d14;">'0/.'</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">similar</span> <span class="n" style="color: #333;">VCF</span> <span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1505
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<pre style="margin: 0;">+<span id="LC1505" class="line" lang="mosel"><span class="n" style="color: #333;">handled</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">four</span> <span class="n" style="color: #333;">modes</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">supported</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1506
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'error'</span><span class="p">/</span><span class="s1" style="color: #d14;">'e'</span> <span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">)</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">out</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">reports</span> <span class="n" style="color: #333;">line</span> <span class="p">#.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1507
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'haploid'</span><span class="p">/</span><span class="s1" style="color: #d14;">'h'</span> <span class="n" style="color: #333;">treats</span> <span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">haploid</span> <span class="n" style="color: #333;">calls</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1508
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<pre style="margin: 0;">+<span id="LC1508" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'missing'</span><span class="p">/</span><span class="s1" style="color: #d14;">'m'</span> <span class="n" style="color: #333;">treats</span> <span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">missing</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1509
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<pre style="margin: 0;">+<span id="LC1509" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'reference'</span><span class="p">/</span><span class="s1" style="color: #d14;">'r'</span> <span class="n" style="color: #333;">treats</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">as</span> <span class="m" style="color: #099;">0.</span></span>
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1510
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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1511
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">oxford</span><span class="p">\-</span><span class="n" style="color: #333;">single</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">chr</span> <span class="n" style="color: #333;">nm</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">single</span><span class="p">\-</span><span class="n" style="color: #333;">chromosome</span> <span class="p">.</span><span class="n" style="color: #333;">gen</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1512
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="mosel"><span class="n" style="color: #333;">ignorable</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">column</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1513
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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1514
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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">oxford</span><span class="p">\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\-</span><span class="n" style="color: #333;">name</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">col</span> <span class="n" style="color: #333;">nm</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Import</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">phenotype</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="p">.</span><span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">hard</span><span class="p">\-</span><span class="n" style="color: #333;">call</span><span class="p">\-</span><span class="n" style="color: #333;">threshold</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1517
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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">Oxford</span><span class="p">\-</span><span class="n" style="color: #333;">format</span> <span class="n" style="color: #333;">fileset</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">loaded</span><span class="p">,</span> <span class="n" style="color: #333;">calls</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1518
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">hard</span><span class="p">\-</span><span class="n" style="color: #333;">call</span><span class="p">\-</span><span class="n" style="color: #333;">threshold</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="nb" style="color: #0086b3;">random</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1520
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="mosel"><span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">uncertainty</span> <span class="n" style="color: #333;">level</span> <span class="n" style="color: #333;">greater</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">0.1</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1521
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="mosel"><span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">treated</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">missing</span><span class="p">.</span> <span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">adjust</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="mosel"><span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">threshold</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">providing</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">numeric</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="mosel"><span class="n" style="color: #333;">parameter</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">randomize</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">calls</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1524
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<pre style="margin: 0;">+<span id="LC1524" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'random'</span><span class="p">.</span></span>
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1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1526
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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">code</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="k" style="font-weight: 600;">string</span> <span class="k" style="font-weight: 600;">list</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Comma</span><span class="p">\-</span><span class="n" style="color: #333;">delimited</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">phenotype</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1528
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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">alias</span><span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">missing_code</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="mosel"><span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">Oxford</span><span class="p">\-</span><span class="n" style="color: #333;">format</span> <span class="n" style="color: #333;">filesets</span> <span class="p">(</span><span class="n" style="color: #333;">def</span><span class="p">.</span> <span class="s1" style="color: #d14;">'NA'</span><span class="p">).</span></span>
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1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1531
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<pre style="margin: 0;">+<span id="LC1531" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\-</span><span class="n" style="color: #333;">ncases</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">num</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1532
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">case</span> <span class="k" style="font-weight: 600;">count</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">1000</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\-</span><span class="n" style="color: #333;">ncontrols</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">control</span> <span class="k" style="font-weight: 600;">count</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">1000</span><span class="p">).</span></span>
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1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\-</span><span class="n" style="color: #333;">prevalence</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">p</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">disease</span> <span class="n" style="color: #333;">prevalence</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.01</span><span class="p">).</span></span>
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1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1539
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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\-</span><span class="n" style="color: #333;">n</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">num</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1540
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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\-</span><span class="n" style="color: #333;">qt</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">sample</span> <span class="k" style="font-weight: 600;">count</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">1000</span><span class="p">).</span></span>
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1541
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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1542
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<pre style="margin: 0;">+<span id="LC1542" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\-</span><span class="n" style="color: #333;">label</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">prefix</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">[\-</span><span class="n" style="color: #333;">qt</span><span class="p">]\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">FID</span><span class="p">/</span><span class="n" style="color: #333;">IID</span> <span class="n" style="color: #333;">name</span> <span class="n" style="color: #333;">prefix</span><span class="p">.</span></span>
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1543
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<pre style="margin: 0;">+<span id="LC1543" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1544
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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">freq</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">simulate</span><span class="p">[\-</span><span class="n" style="color: #333;">qt</span><span class="p">]\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">frequency</span><span class="p">.</span></span>
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1545
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1546
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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">allow</span><span class="p">\-</span><span class="n" style="color: #333;">extra</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'0'</span><span class="p">]</span></span>
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1547
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<pre style="margin: 0;">+<span id="LC1547" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Permit</span> <span class="n" style="color: #333;">unrecognized</span> <span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">codes</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'0'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1548
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<pre style="margin: 0;">+<span id="LC1548" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1549
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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">alias</span><span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">aec</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1550
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<pre style="margin: 0;">+<span id="LC1550" class="line" lang="mosel"><span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">treated</span> <span class="k" style="font-weight: 600;">as</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">had</span></span>
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1551
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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="mosel"><span class="n" style="color: #333;">been</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">zero</span><span class="p">.</span></span>
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1552
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<pre style="margin: 0;">+<span id="LC1552" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1553
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<pre style="margin: 0;">+<span id="LC1553" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">chr</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">autosome</span> <span class="n" style="color: #333;">ct</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-x'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-y'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-xy'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-mt'</span><span class="p">]</span> <span class="p">:</span></span>
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1554
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<pre style="margin: 0;">+<span id="LC1554" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<pre style="margin: 0;">+<span id="LC1555" class="line" lang="mosel"><span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">nonhuman</span> <span class="n" style="color: #333;">chromosome</span> <span class="k" style="font-weight: 600;">set</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1556
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<pre style="margin: 0;">+<span id="LC1556" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">parameter</span> <span class="n" style="color: #333;">sets</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span></span>
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1557
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<pre style="margin: 0;">+<span id="LC1557" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1558
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<pre style="margin: 0;">+<span id="LC1558" class="line" lang="mosel"><span class="n" style="color: #333;">diploid</span> <span class="n" style="color: #333;">autosome</span> <span class="n" style="color: #333;">pairs</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">positive</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">haploid</span> <span class="n" style="color: #333;">chromosomes</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">negative</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1559
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<pre style="margin: 0;">+<span id="LC1559" class="line" lang="mosel"><span class="n" style="color: #333;">Given</span> <span class="n" style="color: #333;">diploid</span> <span class="n" style="color: #333;">autosomes</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">remaining</span> <span class="n" style="color: #333;">modifiers</span> <span class="n" style="color: #333;">indicate</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">absence</span> <span class="k" style="font-weight: 600;">of</span></span>
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1560
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<pre style="margin: 0;">+<span id="LC1560" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">non</span><span class="p">\-</span><span class="n" style="color: #333;">autosomal</span> <span class="n" style="color: #333;">chromosomes</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1561
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<pre style="margin: 0;">+<span id="LC1561" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1562
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<pre style="margin: 0;">+<span id="LC1562" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">cow</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">dog</span><span class="p">/\-\-</span><span class="n" style="color: #333;">horse</span><span class="p">/\-\-</span><span class="n" style="color: #333;">mouse</span><span class="p">/\-\-</span><span class="n" style="color: #333;">rice</span><span class="p">/\-\-</span><span class="n" style="color: #333;">sheep</span> <span class="p">:</span> <span class="n" style="color: #333;">Shortcuts</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">species</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1563
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<pre style="margin: 0;">+<span id="LC1563" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">autosome</span><span class="p">\-</span><span class="n" style="color: #333;">num</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">value</span><span class="p">></span></span>
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1565
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Alias</span> <span class="n" style="color: #333;">for</span> <span class="s2" style="color: #d14;">"\-\-chr\-set <value> no\-y no\-xy no\-mt"</span><span class="p">.</span></span>
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1566
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<pre style="margin: 0;">+<span id="LC1566" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1567
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<pre style="margin: 0;">+<span id="LC1567" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">cm</span><span class="p">\-</span><span class="n" style="color: #333;">map</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">fname</span> <span class="n" style="color: #333;">pattern</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">chr</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">SHAPEIT</span><span class="p">\-</span><span class="n" style="color: #333;">format</span> <span class="n" style="color: #333;">recombination</span> <span class="n" style="color: #333;">maps</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">set</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1568
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<pre style="margin: 0;">+<span id="LC1568" class="line" lang="mosel"><span class="n" style="color: #333;">centimorgan</span> <span class="n" style="color: #333;">positions</span><span class="p">.</span> <span class="k" style="font-weight: 600;">To</span> <span class="n" style="color: #333;">process</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1569
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<pre style="margin: 0;">+<span id="LC1569" class="line" lang="mosel"><span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">chromosome</span><span class="p">,</span> <span class="k" style="font-weight: 600;">include</span> <span class="n" style="color: #333;">a</span> <span class="s1" style="color: #d14;">'@'</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1570
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<pre style="margin: 0;">+<span id="LC1570" class="line" lang="mosel"><span class="n" style="color: #333;">parameter</span> <span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">chrom</span><span class="p">.</span> <span class="n" style="color: #333;">number</span> <span class="n" style="color: #333;">belongs</span><span class="p">,</span></span>
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1571
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="mosel"><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="s1" style="color: #d14;">'genetic_map_chr@_combined_b37.txt'</span><span class="p">.</span></span>
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1572
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">zero</span><span class="p">\-</span><span class="n" style="color: #333;">cms</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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1574
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Zero</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">centimorgan</span> <span class="n" style="color: #333;">positions</span><span class="p">.</span></span>
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1575
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1576
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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">allow</span><span class="p">\-</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">samples</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">:</span> <span class="n" style="color: #333;">Allow</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">fileset</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">samples</span><span class="p">.</span></span>
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1577
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<pre style="margin: 0;">+<span id="LC1577" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1578
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<pre style="margin: 0;">+<span id="LC1578" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">allow</span><span class="p">\-</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">vars</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1579
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<pre style="margin: 0;">+<span id="LC1579" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Allow</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">fileset</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">variants</span><span class="p">.</span></span>
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1580
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<pre style="margin: 0;">+<span id="LC1580" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1581
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<pre style="margin: 0;">+<span id="LC1581" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">fname</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1582
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<pre style="margin: 0;">+<span id="LC1582" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Load</span> <span class="n" style="color: #333;">phenotype</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1583
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<pre style="margin: 0;">+<span id="LC1583" class="line" lang="mosel"><span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">values</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">main</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">fileset</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1584
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<pre style="margin: 0;">+<span id="LC1584" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1585
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<pre style="margin: 0;">+<span id="LC1585" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">all</span><span class="p">\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1586
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<pre style="margin: 0;">+<span id="LC1586" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">basic</span> <span class="n" style="color: #333;">association</span> <span class="n" style="color: #333;">tests</span><span class="p">,</span> <span class="n" style="color: #333;">loop</span> <span class="n" style="color: #333;">through</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">phenotypes</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1587
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<pre style="margin: 0;">+<span id="LC1587" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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1588
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<pre style="margin: 0;">+<span id="LC1588" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1589
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<pre style="margin: 0;">+<span id="LC1589" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mpheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1590
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<pre style="margin: 0;">+<span id="LC1590" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Load</span> <span class="n" style="color: #333;">phenotype</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">column</span> <span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">+</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1591
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<pre style="margin: 0;">+<span id="LC1591" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1592
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<pre style="margin: 0;">+<span id="LC1592" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\-</span><span class="n" style="color: #333;">name</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">c</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">If</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">header</span> <span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1593
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<pre style="margin: 0;">+<span id="LC1593" class="line" lang="mosel"><span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">name</span><span class="p">.</span></span>
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1594
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<pre style="margin: 0;">+<span id="LC1594" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1595
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<pre style="margin: 0;">+<span id="LC1595" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\-</span><span class="n" style="color: #333;">merge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1596
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<pre style="margin: 0;">+<span id="LC1596" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">main</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">fileset</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">phenotype</span> <span class="n" style="color: #333;">value</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1597
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<pre style="margin: 0;">+<span id="LC1597" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">the</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span><span class="p">,</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1598
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<pre style="margin: 0;">+<span id="LC1598" class="line" lang="mosel"><span class="n" style="color: #333;">original</span> <span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">treating</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">phenotype</span> <span class="k" style="font-weight: 600;">as</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1599
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<pre style="margin: 0;">+<span id="LC1599" class="line" lang="mosel"><span class="n" style="color: #333;">missing</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1600
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<pre style="margin: 0;">+<span id="LC1600" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1601
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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">phenotype</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">v</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">phenotype</span> <span class="n" style="color: #333;">value</span> <span class="p">(</span><span class="n" style="color: #333;">normally</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-</span><span class="m" style="color: #099;">9</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1602
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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1603
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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="m" style="color: #099;">1</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1604
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<pre style="margin: 0;">+<span id="LC1604" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Expect</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">phenotypes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">coded</span> <span class="k" style="font-weight: 600;">as</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1605
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<pre style="margin: 0;">+<span id="LC1605" class="line" lang="mosel"><span class="m" style="color: #099;">0</span> <span class="p">=</span> <span class="n" style="color: #333;">control</span><span class="p">,</span> <span class="m" style="color: #099;">1</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">case</span><span class="p">,</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">usual</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1606
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<pre style="margin: 0;">+<span id="LC1606" class="line" lang="mosel"><span class="m" style="color: #099;">0</span> <span class="p">=</span> <span class="n" style="color: #333;">missing</span><span class="p">,</span> <span class="m" style="color: #099;">1</span> <span class="p">=</span> <span class="n" style="color: #333;">control</span><span class="p">,</span> <span class="m" style="color: #099;">2</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">case</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">also</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1607
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<pre style="margin: 0;">+<span id="LC1607" class="line" lang="mosel"><span class="n" style="color: #333;">forces</span> <span class="n" style="color: #333;">phenotypes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">interpreted</span> <span class="k" style="font-weight: 600;">as</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">ctrl</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1608
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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">fn</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Define</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">new</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">phenotype</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">val</span></span>
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1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="mosel"><span class="n" style="color: #333;">parameter</span> <span class="n" style="color: #333;">is</span> <span class="s1" style="color: #d14;">'*'</span><span class="p">,</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">samples</span> <span class="n" style="color: #333;">listed</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1612
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="mosel"><span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">cases</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">everyone</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">control</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1613
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<pre style="margin: 0;">+<span id="LC1613" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">Note</span> <span class="n" style="color: #333;">that</span><span class="p">,</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">shells</span><span class="p">,</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">necessary</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="mosel"><span class="n" style="color: #333;">surround</span> <span class="n" style="color: #333;">the</span> <span class="p">*</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">quotes</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1615
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<pre style="margin: 0;">+<span id="LC1615" class="line" lang="mosel"><span class="n" style="color: #333;">Otherwise</span><span class="p">,</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">third</span> <span class="n" style="color: #333;">column</span> <span class="n" style="color: #333;">entry</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1616
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<pre style="margin: 0;">+<span id="LC1616" class="line" lang="mosel"><span class="n" style="color: #333;">equal</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">val</span> <span class="n" style="color: #333;">parameter</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">cases</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">other</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1617
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<pre style="margin: 0;">+<span id="LC1617" class="line" lang="mosel"><span class="n" style="color: #333;">samples</span> <span class="n" style="color: #333;">mentioned</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">controls</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1618
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<pre style="margin: 0;">+<span id="LC1618" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1619
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<pre style="margin: 0;">+<span id="LC1619" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">tail</span><span class="p">\-</span><span class="n" style="color: #333;">pheno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">Lt</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">Hbt</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Downcode</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">scalar</span> <span class="n" style="color: #333;">phenotype</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1620
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<pre style="margin: 0;">+<span id="LC1620" class="line" lang="mosel"><span class="n" style="color: #333;">phenotype</span><span class="p">.</span> <span class="n" style="color: #333;">All</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">phenotype</span> <span class="n" style="color: #333;">values</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1621
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<pre style="margin: 0;">+<span id="LC1621" class="line" lang="mosel"><span class="n" style="color: #333;">greater</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">Hbt</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">cases</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">all</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">values</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1622
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<pre style="margin: 0;">+<span id="LC1622" class="line" lang="mosel"><span class="n" style="color: #333;">less</span> <span class="n" style="color: #333;">than</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">equal</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Lt</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">controls</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">Hbt</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1623
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<pre style="margin: 0;">+<span id="LC1623" class="line" lang="mosel"><span class="n" style="color: #333;">unspecified</span><span class="p">,</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">equal</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Lt</span><span class="p">;</span> <span class="n" style="color: #333;">otherwise</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span><span class="p">\-</span><span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">phenotype</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">missing</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1625
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1626
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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'keep\-pheno\-on\-missing\-cov'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1627
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<pre style="margin: 0;">+<span id="LC1627" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1628
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\-</span><span class="n" style="color: #333;">name</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><...></span></span>
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1629
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">covariate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">name</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1630
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="mosel"><span class="n" style="color: #333;">Separate</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">spaces</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">commas</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1631
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<pre style="margin: 0;">+<span id="LC1631" class="line" lang="mosel"><span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">dashes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">designate</span> <span class="n" style="color: #333;">ranges</span><span class="p">.</span></span>
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1632
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<pre style="margin: 0;">+<span id="LC1632" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1633
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\-</span><span class="n" style="color: #333;">number</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1634
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">covariate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">index</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1635
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<pre style="margin: 0;">+<span id="LC1635" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1636
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<pre style="margin: 0;">+<span id="LC1636" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">const</span><span class="p">\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1637
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<pre style="margin: 0;">+<span id="LC1637" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">constant</span> <span class="n" style="color: #333;">covariates</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1638
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1639
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<pre style="margin: 0;">+<span id="LC1639" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">allow</span><span class="p">\-</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">covars</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1640
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Allow</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">covariates</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">loaded</span> <span class="k" style="font-weight: 600;">from</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">covar</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1641
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<pre style="margin: 0;">+<span id="LC1641" class="line" lang="mosel"><span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1642
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<pre style="margin: 0;">+<span id="LC1642" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1643
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<pre style="margin: 0;">+<span id="LC1643" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">within</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'keep\-NA'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">initial</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">assignments</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1644
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<pre style="margin: 0;">+<span id="LC1644" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1645
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<pre style="margin: 0;">+<span id="LC1645" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mwithin</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1646
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<pre style="margin: 0;">+<span id="LC1646" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Load</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">assignments</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">column</span> <span class="n" style="color: #333;">n</span><span class="p">+</span><span class="m" style="color: #099;">2.</span></span>
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1647
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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1648
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<pre style="margin: 0;">+<span id="LC1648" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">family</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1649
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<pre style="margin: 0;">+<span id="LC1649" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Create</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">family</span> <span class="n" style="color: #333;">ID</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1650
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<pre style="margin: 0;">+<span id="LC1650" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1651
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<pre style="margin: 0;">+<span id="LC1651" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">loop</span><span class="p">\-</span><span class="n" style="color: #333;">assoc</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'keep\-NA'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1652
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<pre style="margin: 0;">+<span id="LC1652" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Run</span> <span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">case</span><span class="p">/</span><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">association</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1653
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<pre style="margin: 0;">+<span id="LC1653" class="line" lang="mosel"><span class="n" style="color: #333;">commands</span> <span class="n" style="color: #333;">once</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">cluster</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1654
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<pre style="margin: 0;">+<span id="LC1654" class="line" lang="mosel"><span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">membership</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">phenotype</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1655
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<pre style="margin: 0;">+<span id="LC1655" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1656
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<pre style="margin: 0;">+<span id="LC1656" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1657
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<pre style="margin: 0;">+<span id="LC1657" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Load</span> <span class="n" style="color: #333;">sets</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">a</span> <span class="p">.</span><span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1658
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<pre style="margin: 0;">+<span id="LC1658" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1659
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<pre style="margin: 0;">+<span id="LC1659" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">names</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1660
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<pre style="margin: 0;">+<span id="LC1660" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Load</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">sets</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">line</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1661
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<pre style="margin: 0;">+<span id="LC1661" class="line" lang="mosel"><span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">spaces</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">separate</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">names</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1662
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<pre style="margin: 0;">+<span id="LC1662" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1663
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<pre style="margin: 0;">+<span id="LC1663" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">subset</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1664
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<pre style="margin: 0;">+<span id="LC1664" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Load</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">sets</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1665
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<pre style="margin: 0;">+<span id="LC1665" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1666
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<pre style="margin: 0;">+<span id="LC1666" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">collapse</span><span class="p">\-</span><span class="n" style="color: #333;">all</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">name</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Merge</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">sets</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1667
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<pre style="margin: 0;">+<span id="LC1667" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1668
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<pre style="margin: 0;">+<span id="LC1668" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">complement</span><span class="p">\-</span><span class="n" style="color: #333;">sets</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1669
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<pre style="margin: 0;">+<span id="LC1669" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Invert</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">sets</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Names</span> <span class="n" style="color: #333;">gain</span> <span class="s1" style="color: #d14;">'C_'</span> <span class="n" style="color: #333;">prefixes</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1670
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<pre style="margin: 0;">+<span id="LC1670" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1671
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<pre style="margin: 0;">+<span id="LC1671" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">complement</span><span class="p">\-</span><span class="n" style="color: #333;">all</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">s</span><span class="p">></span> <span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">collapse</span><span class="p">\-</span><span class="n" style="color: #333;">all</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">+</span> <span class="n" style="color: #333;">inversion</span><span class="p">.</span></span>
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1672
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<pre style="margin: 0;">+<span id="LC1672" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1673
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<pre style="margin: 0;">+<span id="LC1673" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1674
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<pre style="margin: 0;">+<span id="LC1674" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Define</span> <span class="n" style="color: #333;">sets</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">bp</span> <span class="n" style="color: #333;">ranges</span><span class="p">.</span></span>
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1675
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<pre style="margin: 0;">+<span id="LC1675" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1676
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<pre style="margin: 0;">+<span id="LC1676" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">border</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">kbs</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1677
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<pre style="margin: 0;">+<span id="LC1677" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Stretch</span> <span class="n" style="color: #333;">regions</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1678
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<pre style="margin: 0;">+<span id="LC1678" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1679
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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">collapse</span><span class="p">\-</span><span class="n" style="color: #333;">group</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1680
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<pre style="margin: 0;">+<span id="LC1680" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Define</span> <span class="n" style="color: #333;">sets</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">groups</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">sets</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1681
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<pre style="margin: 0;">+<span id="LC1681" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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1682
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<pre style="margin: 0;">+<span id="LC1682" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1683
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<pre style="margin: 0;">+<span id="LC1683" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">keep</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1684
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<pre style="margin: 0;">+<span id="LC1684" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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1685
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<pre style="margin: 0;">+<span id="LC1685" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1686
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<pre style="margin: 0;">+<span id="LC1686" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">remove</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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1687
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<pre style="margin: 0;">+<span id="LC1687" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">samples</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1688
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<pre style="margin: 0;">+<span id="LC1688" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1689
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<pre style="margin: 0;">+<span id="LC1689" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">keep</span><span class="p">\-</span><span class="n" style="color: #333;">fam</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1690
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<pre style="margin: 0;">+<span id="LC1690" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">families</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1691
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<pre style="margin: 0;">+<span id="LC1691" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1692
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<pre style="margin: 0;">+<span id="LC1692" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">remove</span><span class="p">\-</span><span class="n" style="color: #333;">fam</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">families</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1693
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<pre style="margin: 0;">+<span id="LC1693" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1694
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<pre style="margin: 0;">+<span id="LC1694" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">extract</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'range'</span><span class="p">]</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1695
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<pre style="margin: 0;">+<span id="LC1695" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1696
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<pre style="margin: 0;">+<span id="LC1696" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">exclude</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'range'</span><span class="p">]</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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1697
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<pre style="margin: 0;">+<span id="LC1697" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1698
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<pre style="margin: 0;">+<span id="LC1698" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">keep</span><span class="p">\-</span><span class="n" style="color: #333;">clusters</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1699
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<pre style="margin: 0;">+<span id="LC1699" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">individually</span> <span class="k" style="font-weight: 600;">or</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1701
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<pre style="margin: 0;">+<span id="LC1701" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">keep</span><span class="p">\-</span><span class="n" style="color: #333;">cluster</span><span class="p">\-</span><span class="n" style="color: #333;">names</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="mosel"><span class="n" style="color: #333;">combination</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">define</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1703
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="mosel"><span class="n" style="color: #333;">clusters</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">keep</span><span class="p">;</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">not</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="mosel"><span class="n" style="color: #333;">cluster</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">excluded</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1705
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<pre style="margin: 0;">+<span id="LC1705" class="line" lang="mosel"><span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">spaces</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">separate</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">names</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">keep</span><span class="p">\-</span><span class="n" style="color: #333;">cluster</span><span class="p">\-</span><span class="n" style="color: #333;">names</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1708
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<pre style="margin: 0;">+<span id="LC1708" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">remove</span><span class="p">\-</span><span class="n" style="color: #333;">clusters</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1709
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<pre style="margin: 0;">+<span id="LC1709" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">clusters</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1710
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<pre style="margin: 0;">+<span id="LC1710" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1711
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<pre style="margin: 0;">+<span id="LC1711" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">remove</span><span class="p">\-</span><span class="n" style="color: #333;">cluster</span><span class="p">\-</span><span class="n" style="color: #333;">names</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...></span> <span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">clusters</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1712
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<pre style="margin: 0;">+<span id="LC1712" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1713
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<pre style="margin: 0;">+<span id="LC1713" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">sets</span><span class="p">...></span> <span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">not</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">line</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1714
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<pre style="margin: 0;">+<span id="LC1714" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">Separate</span> <span class="n" style="color: #333;">multiple</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">spaces</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1715
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<pre style="margin: 0;">+<span id="LC1715" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1716
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="n" style="color: #333;">all</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1717
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<pre style="margin: 0;">+<span id="LC1717" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">aren</span><span class="s1" style="color: #d14;">'t a member of any set. (PLINK</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1718
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<pre style="margin: 0;">+<span id="LC1718" class="line" lang="mosel"><span class="s1" style="color: #d14;">1.07 automatically did this under some circumstances.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1719
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<pre style="margin: 0;">+<span id="LC1719" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1720
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<pre style="margin: 0;">+<span id="LC1720" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-attrib\fR <f> [att lst] : Given a file assigning attributes to variants, and a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1721
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<pre style="margin: 0;">+<span id="LC1721" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1722
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<pre style="margin: 0;">+<span id="LC1722" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-attrib\-indiv\fR <f> [a]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1723
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<pre style="margin: 0;">+<span id="LC1723" class="line" lang="mosel"><span class="s1" style="color: #d14;">comma\-delimited list (with no whitespace) of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1724
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<pre style="margin: 0;">+<span id="LC1724" class="line" lang="mosel"><span class="s1" style="color: #d14;">attribute names, remove variants/samples which are</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1725
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="mosel"><span class="s1" style="color: #d14;">either missing from the file or don'</span><span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">any</span> <span class="k" style="font-weight: 600;">of</span></span>
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1726
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">listed</span> <span class="n" style="color: #333;">attributes</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">attribute</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1727
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<pre style="margin: 0;">+<span id="LC1727" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">preceded</span> <span class="n" style="color: #333;">by</span> <span class="s1" style="color: #d14;">'\-'</span><span class="p">,</span> <span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">treated</span> <span class="k" style="font-weight: 600;">as</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1728
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="mosel"><span class="s2" style="color: #d14;">"negative match conditions"</span> <span class="n" style="color: #333;">instead</span><span class="p">:</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1729
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<pre style="margin: 0;">+<span id="LC1729" class="line" lang="mosel"><span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">least</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">negative</span> <span class="n" style="color: #333;">match</span> <span class="n" style="color: #333;">attribute</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">removed</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1730
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<pre style="margin: 0;">+<span id="LC1730" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">character</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">a</span> <span class="s1" style="color: #d14;">'\-'</span><span class="p">,</span> <span class="n" style="color: #333;">due</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1731
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<pre style="margin: 0;">+<span id="LC1731" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">how</span> <span class="nf" style="color: #900; font-weight: 600;">command</span><span class="p">\-</span><span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">parsing</span> <span class="n" style="color: #333;">works</span><span class="p">;</span> <span class="n" style="color: #333;">add</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">comma</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1732
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="mosel"><span class="n" style="color: #333;">front</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">around</span> <span class="n" style="color: #333;">this</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1733
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">chr</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">chrs</span><span class="p">...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1735
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<pre style="margin: 0;">+<span id="LC1735" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">chromosome</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1736
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<pre style="margin: 0;">+<span id="LC1736" class="line" lang="mosel"><span class="n" style="color: #333;">Valid</span> <span class="n" style="color: #333;">choices</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">humans</span> <span class="n" style="color: #333;">are</span> <span class="m" style="color: #099;">0</span> <span class="p">(</span><span class="n" style="color: #333;">unplaced</span><span class="p">),</span> <span class="m" style="color: #099;">1</span><span class="p">\-</span><span class="m" style="color: #099;">22</span><span class="p">,</span> <span class="n" style="color: #333;">X</span><span class="p">,</span> <span class="n" style="color: #333;">Y</span><span class="p">,</span> <span class="n" style="color: #333;">XY</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1737
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<pre style="margin: 0;">+<span id="LC1737" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">MT</span><span class="p">.</span> <span class="n" style="color: #333;">Separate</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">chromosomes</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">spaces</span> <span class="k" style="font-weight: 600;">and</span><span class="p">/</span><span class="k" style="font-weight: 600;">or</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1738
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<pre style="margin: 0;">+<span id="LC1738" class="line" lang="mosel"><span class="n" style="color: #333;">commas</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">dash</span> <span class="p">(</span><span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">adjacent</span> <span class="n" style="color: #333;">spaces</span> <span class="n" style="color: #333;">permitted</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1739
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<pre style="margin: 0;">+<span id="LC1739" class="line" lang="mosel"><span class="n" style="color: #333;">denote</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">range</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="s2" style="color: #d14;">"\-\-chr 1\-4, 22, xy"</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1740
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<pre style="margin: 0;">+<span id="LC1740" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1741
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<pre style="margin: 0;">+<span id="LC1741" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">not</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1742
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<pre style="margin: 0;">+<span id="LC1742" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Reverse</span> <span class="k" style="font-weight: 600;">of</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">chr</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">(</span><span class="n" style="color: #333;">exclude</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">listed</span> <span class="n" style="color: #333;">chromosomes</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1743
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<pre style="margin: 0;">+<span id="LC1743" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1744
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">autosome</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">non</span><span class="p">\-</span><span class="n" style="color: #333;">autosomal</span> <span class="n" style="color: #333;">variants</span><span class="p">.</span></span>
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1746
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<pre style="margin: 0;">+<span id="LC1746" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">autosome</span><span class="p">\-</span><span class="n" style="color: #333;">xy</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1748
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<pre style="margin: 0;">+<span id="LC1748" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">non</span><span class="p">\-</span><span class="n" style="color: #333;">autosomal</span> <span class="n" style="color: #333;">variants</span><span class="p">,</span> <span class="n" style="color: #333;">except</span> <span class="n" style="color: #333;">those</span> <span class="k" style="font-weight: 600;">with</span></span>
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1749
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="mosel"><span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">XY</span> <span class="p">(</span><span class="n" style="color: #333;">pseudo</span><span class="p">\-</span><span class="n" style="color: #333;">autosomal</span> <span class="n" style="color: #333;">region</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">X</span><span class="p">).</span></span>
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1750
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1751
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<pre style="margin: 0;">+<span id="LC1751" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">snps</span><span class="p">\-</span><span class="n" style="color: #333;">only</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'just\-acgt'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">non</span><span class="p">\-</span><span class="n" style="color: #333;">SNP</span> <span class="n" style="color: #333;">variants</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1752
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<pre style="margin: 0;">+<span id="LC1752" class="line" lang="mosel"><span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">SNP</span> <span class="p">=</span> <span class="n" style="color: #333;">both</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1753
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<pre style="margin: 0;">+<span id="LC1753" class="line" lang="mosel"><span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">codes</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">single</span><span class="p">\-</span><span class="n" style="color: #333;">character</span><span class="p">;</span> <span class="s1" style="color: #d14;">'just\-acgt'</span></span>
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1754
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<pre style="margin: 0;">+<span id="LC1754" class="line" lang="mosel"><span class="n" style="color: #333;">restricts</span> <span class="n" style="color: #333;">codes</span> <span class="k" style="font-weight: 600;">to</span> <span class="p">{</span><span class="n" style="color: #333;">A</span><span class="p">,</span><span class="n" style="color: #333;">C</span><span class="p">,</span><span class="n" style="color: #333;">G</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">,</span><span class="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="p">,<</span><span class="n" style="color: #333;">missing</span><span class="p">>}.</span></span>
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1755
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<pre style="margin: 0;">+<span id="LC1755" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1756
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<pre style="margin: 0;">+<span id="LC1756" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">from</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">var</span> <span class="n" style="color: #333;">ID</span><span class="p">></span></span>
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1757
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<pre style="margin: 0;">+<span id="LC1757" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">ID</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variant</span> <span class="k" style="font-weight: 600;">range</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">load</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">used</span></span>
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1758
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1759
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<pre style="margin: 0;">+<span id="LC1759" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">to</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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1760
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">var</span> <span class="n" style="color: #333;">ID</span><span class="p">></span> <span class="n" style="color: #333;">together</span><span class="p">,</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">chromosome</span><span class="p">.</span></span>
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1761
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<pre style="margin: 0;">+<span id="LC1761" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1762
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<pre style="margin: 0;">+<span id="LC1762" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">snp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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1763
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">var</span> <span class="n" style="color: #333;">ID</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">variant</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">load</span><span class="p">.</span></span>
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1764
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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1765
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<pre style="margin: 0;">+<span id="LC1765" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">exclude</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">variant</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">exclude</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1766
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<pre style="margin: 0;">+<span id="LC1766" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1767
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<pre style="margin: 0;">+<span id="LC1767" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">window</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1768
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<pre style="margin: 0;">+<span id="LC1768" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">kbs</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">With</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">snp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">or</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">exclude</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">,</span> <span class="n" style="color: #333;">loads</span><span class="p">/</span><span class="n" style="color: #333;">excludes</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">variants</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1769
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<pre style="margin: 0;">+<span id="LC1769" class="line" lang="mosel"><span class="n" style="color: #333;">within</span> <span class="n" style="color: #333;">half</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">kb</span> <span class="n" style="color: #333;">distance</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">one</span><span class="p">.</span></span>
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1770
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<pre style="margin: 0;">+<span id="LC1770" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1771
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<pre style="margin: 0;">+<span id="LC1771" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">from</span><span class="p">\-</span><span class="n" style="color: #333;">bp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">pos</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1772
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<pre style="margin: 0;">+<span id="LC1772" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">physical</span> <span class="n" style="color: #333;">position</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">define</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variant</span> <span class="k" style="font-weight: 600;">range</span> <span class="k" style="font-weight: 600;">to</span></span>
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1773
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<pre style="margin: 0;">+<span id="LC1773" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1774
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<pre style="margin: 0;">+<span id="LC1774" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">to</span><span class="p">\-</span><span class="n" style="color: #333;">bp</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1775
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<pre style="margin: 0;">+<span id="LC1775" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">pos</span><span class="p">></span> <span class="nf" style="color: #900; font-weight: 600;">load</span><span class="p">.</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">from</span><span class="p">\-</span><span class="n" style="color: #333;">kb</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="k" style="font-weight: 600;">to</span><span class="p">\-</span><span class="n" style="color: #333;">kb</span><span class="p">/\-\-</span><span class="k" style="font-weight: 600;">from</span><span class="p">\-</span><span class="n" style="color: #333;">mb</span><span class="p">/\-\-</span><span class="k" style="font-weight: 600;">to</span><span class="p">\-</span><span class="n" style="color: #333;">mb</span> <span class="n" style="color: #333;">allow</span> <span class="n" style="color: #333;">decimal</span></span>
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1776
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<pre style="margin: 0;">+<span id="LC1776" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1777
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<pre style="margin: 0;">+<span id="LC1777" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">from</span><span class="p">\-</span><span class="n" style="color: #333;">kb</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">pos</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1778
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<pre style="margin: 0;">+<span id="LC1778" class="line" lang="mosel"><span class="n" style="color: #333;">values</span><span class="p">.</span> <span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">chromosome</span> <span class="p">(</span><span class="n" style="color: #333;">using</span></span>
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1779
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<pre style="margin: 0;">+<span id="LC1779" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1780
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<pre style="margin: 0;">+<span id="LC1780" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">to</span><span class="p">\-</span><span class="n" style="color: #333;">kb</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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1781
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<pre style="margin: 0;">+<span id="LC1781" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">pos</span><span class="p">></span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">chr</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">flags</span><span class="p">.</span></span>
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1782
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<pre style="margin: 0;">+<span id="LC1782" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1783
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<pre style="margin: 0;">+<span id="LC1783" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">from</span><span class="p">\-</span><span class="n" style="color: #333;">mb</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">pos</span><span class="p">></span></span>
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1784
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<pre style="margin: 0;">+<span id="LC1784" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1785
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<pre style="margin: 0;">+<span id="LC1785" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">to</span><span class="p">\-</span><span class="n" style="color: #333;">mb</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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1786
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<pre style="margin: 0;">+<span id="LC1786" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">pos</span><span class="p">></span></span>
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1787
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<pre style="margin: 0;">+<span id="LC1787" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1788
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<pre style="margin: 0;">+<span id="LC1788" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">snps</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">var</span> <span class="n" style="color: #333;">IDs</span><span class="p">...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1789
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<pre style="margin: 0;">+<span id="LC1789" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">variant</span> <span class="k" style="font-weight: 600;">range</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">load</span> <span class="k" style="font-weight: 600;">or</span></span>
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1790
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<pre style="margin: 0;">+<span id="LC1790" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1791
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<pre style="margin: 0;">+<span id="LC1791" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">exclude</span><span class="p">\-</span><span class="n" style="color: #333;">snps</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1792
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<pre style="margin: 0;">+<span id="LC1792" class="line" lang="mosel"><span class="n" style="color: #333;">exclude</span><span class="p">.</span> <span class="n" style="color: #333;">E</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="s2" style="color: #d14;">"\-\-snps rs1111\-rs2222, rs3333, rs4444"</span><span class="p">.</span></span>
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1793
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<pre style="margin: 0;">+<span id="LC1793" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1794
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<pre style="margin: 0;">+<span id="LC1794" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">thin</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">p</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1795
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<pre style="margin: 0;">+<span id="LC1795" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Randomly</span> <span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">variants</span><span class="p">,</span> <span class="n" style="color: #333;">retaining</span> <span class="n" style="color: #333;">each</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">prob</span><span class="p">.</span> <span class="n" style="color: #333;">p</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1796
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<pre style="margin: 0;">+<span id="LC1796" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1797
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<pre style="margin: 0;">+<span id="LC1797" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">thin</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Randomly</span> <span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">until</span> <span class="n" style="color: #333;">n</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">them</span> <span class="n" style="color: #333;">remain</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1798
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<pre style="margin: 0;">+<span id="LC1798" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1799
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<pre style="margin: 0;">+<span id="LC1799" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">bp</span><span class="p">\-</span><span class="n" style="color: #333;">space</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">bps</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Remove</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">pair</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">closer</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">the</span></span>
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1800
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<pre style="margin: 0;">+<span id="LC1800" class="line" lang="mosel"><span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">bp</span> <span class="n" style="color: #333;">distance</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Equivalent</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">VCFtools</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">thin</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.)</span></span>
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1801
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<pre style="margin: 0;">+<span id="LC1801" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1802
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<pre style="margin: 0;">+<span id="LC1802" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">thin</span><span class="p">\-</span><span class="n" style="color: #333;">indiv</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">p</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1803
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<pre style="margin: 0;">+<span id="LC1803" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Randomly</span> <span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">retaining</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">prob</span><span class="p">.</span> <span class="n" style="color: #333;">p</span><span class="p">.</span></span>
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1804
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<pre style="margin: 0;">+<span id="LC1804" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1805
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<pre style="margin: 0;">+<span id="LC1805" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">thin</span><span class="p">\-</span><span class="n" style="color: #333;">indiv</span><span class="p">\-</span><span class="k" style="font-weight: 600;">count</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1806
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<pre style="margin: 0;">+<span id="LC1806" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Randomly</span> <span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">until</span> <span class="n" style="color: #333;">n</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">them</span> <span class="n" style="color: #333;">remain</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1807
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<pre style="margin: 0;">+<span id="LC1807" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1808
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<pre style="margin: 0;">+<span id="LC1808" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">filter</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)...></span> <span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">samples</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">a</span> <span class="m" style="color: #099;">3</span><span class="n" style="color: #333;">rd</span> <span class="n" style="color: #333;">column</span> <span class="n" style="color: #333;">entry</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1809
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<pre style="margin: 0;">+<span id="LC1809" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">matching</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span></span>
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1810
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<pre style="margin: 0;">+<span id="LC1810" class="line" lang="mosel"><span class="n" style="color: #333;">space</span><span class="p">\-</span><span class="n" style="color: #333;">separated</span> <span class="n" style="color: #333;">value</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">).</span></span>
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1811
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<pre style="margin: 0;">+<span id="LC1811" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1812
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<pre style="margin: 0;">+<span id="LC1812" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mfilter</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1813
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<pre style="margin: 0;">+<span id="LC1813" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Match</span> <span class="n" style="color: #333;">against</span> <span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">+</span><span class="m" style="color: #099;">2</span><span class="p">)</span><span class="n" style="color: #333;">th</span> <span class="n" style="color: #333;">column</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span></span>
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1814
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<pre style="margin: 0;">+<span id="LC1814" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1815
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<pre style="margin: 0;">+<span id="LC1815" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">geno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">val</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1816
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<pre style="margin: 0;">+<span id="LC1816" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">call</span> <span class="n" style="color: #333;">frequencies</span> <span class="n" style="color: #333;">greater</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1817
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<pre style="margin: 0;">+<span id="LC1817" class="line" lang="mosel"><span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">threshold</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.1</span><span class="p">).</span> <span class="p">(</span><span class="n" style="color: #333;">Note</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1818
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<pre style="margin: 0;">+<span id="LC1818" class="line" lang="mosel"><span class="n" style="color: #333;">threshold</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">applied</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">geno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">invoked</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">a</span></span>
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1819
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<pre style="margin: 0;">+<span id="LC1819" class="line" lang="mosel"><span class="n" style="color: #333;">parameter</span><span class="p">;</span> <span class="n" style="color: #333;">when</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">geno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">invoked</span><span class="p">,</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">per</span><span class="p">\-</span><span class="n" style="color: #333;">variant</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1820
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<pre style="margin: 0;">+<span id="LC1820" class="line" lang="mosel"><span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">call</span> <span class="n" style="color: #333;">frequency</span> <span class="n" style="color: #333;">ceiling</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">enforced</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">all</span><span class="p">.</span> <span class="n" style="color: #333;">Other</span></span>
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1821
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<pre style="margin: 0;">+<span id="LC1821" class="line" lang="mosel"><span class="n" style="color: #333;">inclusion</span><span class="p">/</span><span class="n" style="color: #333;">exclusion</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">thresholds</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">way</span><span class="p">.)</span></span>
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1822
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<pre style="margin: 0;">+<span id="LC1822" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1823
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<pre style="margin: 0;">+<span id="LC1823" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mind</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">val</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1824
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<pre style="margin: 0;">+<span id="LC1824" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">call</span> <span class="n" style="color: #333;">frequencies</span> <span class="n" style="color: #333;">greater</span> <span class="n" style="color: #333;">than</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1825
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<pre style="margin: 0;">+<span id="LC1825" class="line" lang="mosel"><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">threshold</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.1</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1826
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<pre style="margin: 0;">+<span id="LC1826" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1827
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<pre style="margin: 0;">+<span id="LC1827" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">oblig</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f1</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">f2</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">blocks</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">calls</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1828
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<pre style="margin: 0;">+<span id="LC1828" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">geno</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">mind</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">ignore</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">should</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1829
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<pre style="margin: 0;">+<span id="LC1829" class="line" lang="mosel"><span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">block</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1830
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<pre style="margin: 0;">+<span id="LC1830" class="line" lang="mosel"><span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">second</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">should</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1831
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<pre style="margin: 0;">+<span id="LC1831" class="line" lang="mosel"><span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">FIDs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">column</span><span class="p">,</span> <span class="n" style="color: #333;">IIDs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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1832
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<pre style="margin: 0;">+<span id="LC1832" class="line" lang="mosel"><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">block</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">third</span><span class="p">.</span></span>
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1833
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<pre style="margin: 0;">+<span id="LC1833" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1834
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<pre style="margin: 0;">+<span id="LC1834" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">prune</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1835
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<pre style="margin: 0;">+<span id="LC1835" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Remove</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">phenotypes</span><span class="p">.</span></span>
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1836
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<pre style="margin: 0;">+<span id="LC1836" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1837
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<pre style="margin: 0;">+<span id="LC1837" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">maf</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">freq</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1838
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<pre style="margin: 0;">+<span id="LC1838" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">minor</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">frequency</span> <span class="n" style="color: #333;">lower</span> <span class="n" style="color: #333;">than</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1839
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<pre style="margin: 0;">+<span id="LC1839" class="line" lang="mosel"><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">threshold</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.01</span><span class="p">).</span></span>
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1840
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<pre style="margin: 0;">+<span id="LC1840" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1841
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<pre style="margin: 0;">+<span id="LC1841" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">\-</span><span class="n" style="color: #333;">maf</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">freq</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1842
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<pre style="margin: 0;">+<span id="LC1842" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">MAF</span> <span class="n" style="color: #333;">greater</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">threshold</span><span class="p">.</span></span>
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1843
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<pre style="margin: 0;">+<span id="LC1843" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1844
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<pre style="margin: 0;">+<span id="LC1844" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mac</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">ct</span><span class="p">></span></span>
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1845
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<pre style="margin: 0;">+<span id="LC1845" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">minor</span> <span class="n" style="color: #333;">allele</span> <span class="k" style="font-weight: 600;">count</span> <span class="n" style="color: #333;">lower</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">the</span></span>
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1846
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<pre style="margin: 0;">+<span id="LC1846" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1847
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<pre style="margin: 0;">+<span id="LC1847" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">alias</span><span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">min</span><span class="p">\-</span><span class="n" style="color: #333;">ac</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1848
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<pre style="margin: 0;">+<span id="LC1848" class="line" lang="mosel"><span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">threshold</span><span class="p">.</span></span>
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1849
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<pre style="margin: 0;">+<span id="LC1849" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1850
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<pre style="margin: 0;">+<span id="LC1850" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">\-</span><span class="n" style="color: #333;">mac</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">ct</span><span class="p">></span></span>
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1851
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<pre style="margin: 0;">+<span id="LC1851" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">minor</span> <span class="n" style="color: #333;">allele</span> <span class="k" style="font-weight: 600;">count</span> <span class="n" style="color: #333;">greater</span> <span class="n" style="color: #333;">than</span></span>
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1852
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<pre style="margin: 0;">+<span id="LC1852" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1853
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<pre style="margin: 0;">+<span id="LC1853" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">alias</span><span class="p">:</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">\-</span><span class="n" style="color: #333;">ac</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">)</span></span>
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1854
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<pre style="margin: 0;">+<span id="LC1854" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">threshold</span><span class="p">.</span></span>
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1855
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<pre style="margin: 0;">+<span id="LC1855" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1856
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<pre style="margin: 0;">+<span id="LC1856" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">maf</span><span class="p">\-</span><span class="n" style="color: #333;">succ</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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1857
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<pre style="margin: 0;">+<span id="LC1857" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Rule</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">succession</span> <span class="n" style="color: #333;">MAF</span> <span class="n" style="color: #333;">estimation</span> <span class="p">(</span><span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">EIGENSOFT</span><span class="p">).</span></span>
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1858
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<pre style="margin: 0;">+<span id="LC1858" class="line" lang="mosel"><span class="n" style="color: #333;">Given</span> <span class="n" style="color: #333;">j</span> <span class="n" style="color: #333;">observations</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">allele</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">k</span> <span class="p">>=</span> <span class="n" style="color: #333;">j</span> <span class="n" style="color: #333;">observations</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1859
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<pre style="margin: 0;">+<span id="LC1859" class="line" lang="mosel"><span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">infer</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">MAF</span> <span class="k" style="font-weight: 600;">of</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">+</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="p">/</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">+</span><span class="n" style="color: #333;">k</span><span class="p">+</span><span class="m" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">rather</span> <span class="n" style="color: #333;">than</span></span>
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1860
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<pre style="margin: 0;">+<span id="LC1860" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">j</span> <span class="p">/</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">+</span><span class="n" style="color: #333;">k</span><span class="p">).</span></span>
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1861
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<pre style="margin: 0;">+<span id="LC1861" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1862
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<pre style="margin: 0;">+<span id="LC1862" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="nb" style="color: #0086b3;">read</span><span class="p">\-</span><span class="n" style="color: #333;">freq</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">fn</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Estimate</span> <span class="n" style="color: #333;">MAFs</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">heterozygote</span> <span class="n" style="color: #333;">frequencies</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span></span>
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1863
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<pre style="margin: 0;">+<span id="LC1863" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">freq</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">fileset</span><span class="p">.</span></span>
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1864
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<pre style="margin: 0;">+<span id="LC1864" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1865
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<pre style="margin: 0;">+<span id="LC1865" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">hwe</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">p</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'midp'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'include\-nonctrl'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Hardy</span><span class="p">\-</span><span class="n" style="color: #333;">Weinberg</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1866
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<pre style="margin: 0;">+<span id="LC1866" class="line" lang="mosel"><span class="n" style="color: #333;">equilibrium</span> <span class="n" style="color: #333;">exact</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">values</span></span>
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1867
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<pre style="margin: 0;">+<span id="LC1867" class="line" lang="mosel"><span class="n" style="color: #333;">below</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">threshold</span><span class="p">.</span></span>
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1868
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<pre style="margin: 0;">+<span id="LC1868" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1869
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<pre style="margin: 0;">+<span id="LC1869" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">me</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">t</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">v</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'var\-first'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Filter</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">trios</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Mendel</span> <span class="n" style="color: #333;">error</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1870
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<pre style="margin: 0;">+<span id="LC1870" class="line" lang="mosel"><span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">exceeding</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">thresholds</span><span class="p">.</span></span>
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1871
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<pre style="margin: 0;">+<span id="LC1871" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1872
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<pre style="margin: 0;">+<span id="LC1872" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">me</span><span class="p">\-</span><span class="n" style="color: #333;">exclude</span><span class="p">\-</span><span class="n" style="color: #333;">one</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">ratio</span><span class="p">]</span></span>
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1873
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<pre style="margin: 0;">+<span id="LC1873" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Make</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">me</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">exclude</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">per</span> <span class="n" style="color: #333;">trio</span><span class="p">.</span></span>
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1874
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<pre style="margin: 0;">+<span id="LC1874" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1875
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<pre style="margin: 0;">+<span id="LC1875" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">qual</span><span class="p">\-</span><span class="n" style="color: #333;">scores</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">qcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">IDcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">skip</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Filter</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span></span>
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1876
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<pre style="margin: 0;">+<span id="LC1876" class="line" lang="mosel"><span class="n" style="color: #333;">out</span><span class="p">\-</span><span class="k" style="font-weight: 600;">of</span><span class="p">\-</span><span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">quality</span> <span class="n" style="color: #333;">scores</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1877
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<pre style="margin: 0;">+<span id="LC1877" class="line" lang="mosel"><span class="n" style="color: #333;">Default</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="p">[</span><span class="m" style="color: #099;">0</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">einfty</span> <span class="p">).</span></span>
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1878
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<pre style="margin: 0;">+<span id="LC1878" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1879
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<pre style="margin: 0;">+<span id="LC1879" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">qual</span><span class="p">\-</span><span class="n" style="color: #333;">threshold</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="k" style="font-weight: 600;">min</span> <span class="n" style="color: #333;">qual</span> <span class="n" style="color: #333;">score</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1880
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<pre style="margin: 0;">+<span id="LC1880" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">qual</span><span class="p">\-</span><span class="n" style="color: #333;">scores</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">range</span> <span class="nb" style="color: #0086b3;">floor</span><span class="p">.</span></span>
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1881
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<pre style="margin: 0;">+<span id="LC1881" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1882
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<pre style="margin: 0;">+<span id="LC1882" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">qual</span><span class="p">\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">\-</span><span class="n" style="color: #333;">threshold</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="k" style="font-weight: 600;">max</span> <span class="n" style="color: #333;">qual</span> <span class="n" style="color: #333;">score</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1883
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<pre style="margin: 0;">+<span id="LC1883" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">qual</span><span class="p">\-</span><span class="n" style="color: #333;">scores</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">ceiling</span><span class="p">.</span></span>
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1884
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<pre style="margin: 0;">+<span id="LC1884" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1885
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<pre style="margin: 0;">+<span id="LC1885" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">allow</span><span class="p">\-</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1886
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<pre style="margin: 0;">+<span id="LC1886" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Do</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">treat</span> <span class="n" style="color: #333;">ambiguous</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">having</span> <span class="n" style="color: #333;">missing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1887
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<pre style="margin: 0;">+<span id="LC1887" class="line" lang="mosel"><span class="n" style="color: #333;">phenotypes</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">commands</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Automatic</span> <span class="p">\</span><span class="n" style="color: #333;">fI</span><span class="p">\,/</span><span class="n" style="color: #333;">w</span><span class="p">\/\</span><span class="n" style="color: #333;">fP</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.)</span></span>
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1888
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<pre style="margin: 0;">+<span id="LC1888" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1889
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<pre style="margin: 0;">+<span id="LC1889" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">must</span><span class="p">\-</span><span class="n" style="color: #333;">have</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1890
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<pre style="margin: 0;">+<span id="LC1890" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Force</span> <span class="n" style="color: #333;">ambiguous</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span> <span class="n" style="color: #333;">phenotypes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">on</span></span>
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1891
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<pre style="margin: 0;">+<span id="LC1891" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">just</span><span class="p">\-</span><span class="n" style="color: #333;">fam</span><span class="p">/\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">/\-\-</span><span class="nb" style="color: #0086b3;">write</span><span class="p">\-</span><span class="n" style="color: #333;">covar</span><span class="p">.</span></span>
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1892
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<pre style="margin: 0;">+<span id="LC1892" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1893
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<pre style="margin: 0;">+<span id="LC1893" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">filter</span><span class="p">\-</span><span class="n" style="color: #333;">cases</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1894
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<pre style="margin: 0;">+<span id="LC1894" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">cases</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">current</span> <span class="n" style="color: #333;">analysis</span><span class="p">.</span></span>
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1895
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<pre style="margin: 0;">+<span id="LC1895" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1896
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<pre style="margin: 0;">+<span id="LC1896" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">filter</span><span class="p">\-</span><span class="n" style="color: #333;">controls</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1897
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<pre style="margin: 0;">+<span id="LC1897" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">controls</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1898
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<pre style="margin: 0;">+<span id="LC1898" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1899
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<pre style="margin: 0;">+<span id="LC1899" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">filter</span><span class="p">\-</span><span class="n" style="color: #333;">males</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1900
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<pre style="margin: 0;">+<span id="LC1900" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">males</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1901
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<pre style="margin: 0;">+<span id="LC1901" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1902
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<pre style="margin: 0;">+<span id="LC1902" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">filter</span><span class="p">\-</span><span class="n" style="color: #333;">females</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1903
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<pre style="margin: 0;">+<span id="LC1903" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">females</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1904
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<pre style="margin: 0;">+<span id="LC1904" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1905
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<pre style="margin: 0;">+<span id="LC1905" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">filter</span><span class="p">\-</span><span class="n" style="color: #333;">founders</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1906
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<pre style="margin: 0;">+<span id="LC1906" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">founders</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1907
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<pre style="margin: 0;">+<span id="LC1907" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1908
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<pre style="margin: 0;">+<span id="LC1908" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">filter</span><span class="p">\-</span><span class="n" style="color: #333;">nonfounders</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">nonfounders</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1909
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<pre style="margin: 0;">+<span id="LC1909" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1910
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<pre style="margin: 0;">+<span id="LC1910" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">nonfounders</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1911
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<pre style="margin: 0;">+<span id="LC1911" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">nonfounders</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">freq</span><span class="p">/</span><span class="n" style="color: #333;">HWE</span> <span class="n" style="color: #333;">calculations</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1912
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<pre style="margin: 0;">+<span id="LC1912" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1913
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<pre style="margin: 0;">+<span id="LC1913" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">founders</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'require\-2\-missing'</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'first'</span><span class="p">]</span> <span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1914
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<pre style="margin: 0;">+<span id="LC1914" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1915
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<pre style="margin: 0;">+<span id="LC1915" class="line" lang="mosel"><span class="n" style="color: #333;">Clear</span> <span class="n" style="color: #333;">parental</span> <span class="n" style="color: #333;">IDs</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">those</span> <span class="k" style="font-weight: 600;">with</span> <span class="m" style="color: #099;">1</span><span class="p">+</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">parent</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1916
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<pre style="margin: 0;">+<span id="LC1916" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1917
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<pre style="margin: 0;">+<span id="LC1917" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">\-</span><span class="n" style="color: #333;">allele</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">fn</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">With</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">A</span><span class="p">/</span><span class="n" style="color: #333;">A</span><span class="p">\-</span><span class="n" style="color: #333;">transpose</span><span class="p">/</span><span class="n" style="color: #333;">AD</span><span class="p">,</span> <span class="k" style="font-weight: 600;">count</span> <span class="n" style="color: #333;">alleles</span> <span class="n" style="color: #333;">named</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1918
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<pre style="margin: 0;">+<span id="LC1918" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="p">(</span><span class="n" style="color: #333;">otherwise</span> <span class="n" style="color: #333;">A1</span> <span class="n" style="color: #333;">alleles</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">always</span> <span class="n" style="color: #333;">counted</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1919
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<pre style="margin: 0;">+<span id="LC1919" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1920
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<pre style="margin: 0;">+<span id="LC1920" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">output</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">MT</span> <span class="n" style="color: #333;">code</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">coding</span> <span class="n" style="color: #333;">scheme</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">by</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1921
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<pre style="margin: 0;">+<span id="LC1921" class="line" lang="mosel"><span class="n" style="color: #333;">providing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">desired</span> <span class="n" style="color: #333;">human</span> <span class="n" style="color: #333;">mitochondrial</span> <span class="n" style="color: #333;">code</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1922
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<pre style="margin: 0;">+<span id="LC1922" class="line" lang="mosel"><span class="p">(</span><span class="k" style="font-weight: 600;">Options</span> <span class="n" style="color: #333;">are</span> <span class="s1" style="color: #d14;">'26'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'M'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'MT'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'0M'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'chr26'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'chrM'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1923
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<pre style="margin: 0;">+<span id="LC1923" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'chrMT'</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1924
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<pre style="margin: 0;">+<span id="LC1924" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1925
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<pre style="margin: 0;">+<span id="LC1925" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">output</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">genotype</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">ch</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">represent</span> <span class="n" style="color: #333;">missing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1926
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<pre style="margin: 0;">+<span id="LC1926" class="line" lang="mosel"><span class="n" style="color: #333;">genotypes</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">files</span> <span class="p">(</span><span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1927
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">genotype</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">value</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1929
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<pre style="margin: 0;">+<span id="LC1929" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">output</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">phenotype</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">s</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">string</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">represent</span> <span class="n" style="color: #333;">missing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="mosel"><span class="n" style="color: #333;">phenotypes</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">files</span> <span class="p">(</span><span class="n" style="color: #333;">normally</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1931
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<pre style="margin: 0;">+<span id="LC1931" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">phenotype</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">value</span><span class="p">).</span></span>
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1932
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<pre style="margin: 0;">+<span id="LC1932" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1933
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<pre style="margin: 0;">+<span id="LC1933" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">zero</span><span class="p">\-</span><span class="n" style="color: #333;">cluster</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">combination</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">within</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">family</span><span class="p">,</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">blocks</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1934
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<pre style="margin: 0;">+<span id="LC1934" class="line" lang="mosel"><span class="n" style="color: #333;">genotype</span> <span class="n" style="color: #333;">calls</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">missing</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">have</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1935
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<pre style="margin: 0;">+<span id="LC1935" class="line" lang="mosel"><span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cluster</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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1936
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<pre style="margin: 0;">+<span id="LC1936" class="line" lang="mosel"><span class="n" style="color: #333;">second</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">no</span></span>
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1937
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<pre style="margin: 0;">+<span id="LC1937" class="line" lang="mosel"><span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">commands</span><span class="p">.</span></span>
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1938
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<pre style="margin: 0;">+<span id="LC1938" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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1939
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<pre style="margin: 0;">+<span id="LC1939" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">hh</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1940
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<pre style="margin: 0;">+<span id="LC1940" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Cause</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">heterozygous</span></span>
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1941
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<pre style="margin: 0;">+<span id="LC1941" class="line" lang="mosel"><span class="n" style="color: #333;">haploid</span> <span class="n" style="color: #333;">genotypes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">missing</span><span class="p">.</span></span>
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1942
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<pre style="margin: 0;">+<span id="LC1942" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1943
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<pre style="margin: 0;">+<span id="LC1943" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">mixed</span><span class="p">\-</span><span class="n" style="color: #333;">mt</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">:</span> <span class="n" style="color: #333;">Cause</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">mixed</span> <span class="n" style="color: #333;">MT</span></span>
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1944
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<pre style="margin: 0;">+<span id="LC1944" class="line" lang="mosel"><span class="n" style="color: #333;">genotypes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">missing</span><span class="p">.</span></span>
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1945
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<pre style="margin: 0;">+<span id="LC1945" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1946
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<pre style="margin: 0;">+<span id="LC1946" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">split</span><span class="p">\-</span><span class="n" style="color: #333;">x</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">bp1</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">bp2</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-fail'</span><span class="p">]</span></span>
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1947
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<pre style="margin: 0;">+<span id="LC1947" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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1948
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<pre style="margin: 0;">+<span id="LC1948" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">split</span><span class="p">\-</span><span class="n" style="color: #333;">x</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">build</span><span class="p">></span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-fail'</span><span class="p">]</span> <span class="p">:</span></span>
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1949
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<pre style="margin: 0;">+<span id="LC1949" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1950
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<pre style="margin: 0;">+<span id="LC1950" class="line" lang="mosel"><span class="n" style="color: #333;">Changes</span> <span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">code</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">chrX</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">bp</span> <span class="n" style="color: #333;">position</span> <span class="p"><=</span> <span class="n" style="color: #333;">bp1</span> <span class="k" style="font-weight: 600;">or</span> <span class="p">>=</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1951
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<pre style="margin: 0;">+<span id="LC1951" class="line" lang="mosel"><span class="n" style="color: #333;">bp2</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">XY</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">codes</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">supported</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">shorthand</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1952
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<pre style="margin: 0;">+<span id="LC1952" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'b36'</span><span class="p">/</span><span class="s1" style="color: #d14;">'hg18'</span> <span class="p">=</span> <span class="n" style="color: #333;">NCBI</span> <span class="m" style="color: #099;">36</span><span class="p">,</span> <span class="m" style="color: #099;">2709521</span><span class="p">/</span><span class="m" style="color: #099;">154584237</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1953
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<pre style="margin: 0;">+<span id="LC1953" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'b37'</span><span class="p">/</span><span class="s1" style="color: #d14;">'hg19'</span> <span class="p">=</span> <span class="n" style="color: #333;">GRCh37</span><span class="p">,</span> <span class="m" style="color: #099;">2699520</span><span class="p">/</span><span class="m" style="color: #099;">154931044</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1954
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<pre style="margin: 0;">+<span id="LC1954" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'b38'</span><span class="p">/</span><span class="s1" style="color: #d14;">'hg38'</span> <span class="p">=</span> <span class="n" style="color: #333;">GRCh38</span><span class="p">,</span> <span class="m" style="color: #099;">2781479</span><span class="p">/</span><span class="m" style="color: #099;">155701383</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1955
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<pre style="margin: 0;">+<span id="LC1955" class="line" lang="mosel"><span class="n" style="color: #333;">By</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">would</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">affected</span> <span class="n" style="color: #333;">by</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1956
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<pre style="margin: 0;">+<span id="LC1956" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">split</span><span class="p">\-</span><span class="n" style="color: #333;">x</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">;</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'no\-fail'</span> <span class="n" style="color: #333;">modifier</span> <span class="p">(</span><span class="n" style="color: #333;">useful</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">scripts</span><span class="p">)</span> <span class="n" style="color: #333;">overrides</span> <span class="n" style="color: #333;">this</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1957
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<pre style="margin: 0;">+<span id="LC1957" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1958
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<pre style="margin: 0;">+<span id="LC1958" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\-</span><span class="n" style="color: #333;">x</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-fail'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Merge</span> <span class="n" style="color: #333;">XY</span> <span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">back</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">X</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1959
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<pre style="margin: 0;">+<span id="LC1959" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1960
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<pre style="margin: 0;">+<span id="LC1960" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">me</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1961
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<pre style="margin: 0;">+<span id="LC1961" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Cause</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">Mendel</span> <span class="n" style="color: #333;">errors</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">missing</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1962
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<pre style="margin: 0;">+<span id="LC1962" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1963
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<pre style="margin: 0;">+<span id="LC1963" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">fill</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">a2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1964
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<pre style="margin: 0;">+<span id="LC1964" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Cause</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">replace</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">calls</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1965
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<pre style="margin: 0;">+<span id="LC1965" class="line" lang="mosel"><span class="n" style="color: #333;">homozygous</span> <span class="n" style="color: #333;">A2</span> <span class="n" style="color: #333;">calls</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1966
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<pre style="margin: 0;">+<span id="LC1966" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1967
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<pre style="margin: 0;">+<span id="LC1967" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">var</span><span class="p">\-</span><span class="n" style="color: #333;">ids</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">t</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1968
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<pre style="margin: 0;">+<span id="LC1968" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Given</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">template</span> <span class="k" style="font-weight: 600;">string</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="s1" style="color: #d14;">'@'</span> <span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1969
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<pre style="margin: 0;">+<span id="LC1969" class="line" lang="mosel"><span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">go</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'#'</span> <span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bp</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1970
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<pre style="margin: 0;">+<span id="LC1970" class="line" lang="mosel"><span class="n" style="color: #333;">coordinate</span> <span class="n" style="color: #333;">belongs</span><span class="p">,</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">var</span><span class="p">\-</span><span class="n" style="color: #333;">ids</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1971
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<pre style="margin: 0;">+<span id="LC1971" class="line" lang="mosel"><span class="n" style="color: #333;">assigns</span> <span class="n" style="color: #333;">chromosome</span><span class="p">\-</span><span class="k" style="font-weight: 600;">and</span><span class="p">\-</span><span class="n" style="color: #333;">bp</span><span class="p">\-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">unnamed</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1972
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<pre style="margin: 0;">+<span id="LC1972" class="line" lang="mosel"><span class="n" style="color: #333;">variants</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1973
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<pre style="margin: 0;">+<span id="LC1973" class="line" lang="mosel"><span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">use</span> <span class="s1" style="color: #d14;">'$1'</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'$2'</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">refer</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1974
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<pre style="margin: 0;">+<span id="LC1974" class="line" lang="mosel"><span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">template</span> <span class="k" style="font-weight: 600;">string</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1975
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<pre style="margin: 0;">+<span id="LC1975" class="line" lang="mosel"><span class="n" style="color: #333;">fact</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">becomes</span> <span class="n" style="color: #333;">essential</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">multiple</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1976
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<pre style="margin: 0;">+<span id="LC1976" class="line" lang="mosel"><span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">share</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">coordinate</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1977
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<pre style="margin: 0;">+<span id="LC1977" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1978
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<pre style="margin: 0;">+<span id="LC1978" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">new</span><span class="p">\-</span><span class="n" style="color: #333;">id</span><span class="p">\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">\-</span><span class="n" style="color: #333;">allele</span><span class="p">\-</span><span class="n" style="color: #333;">len</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">leading</span> <span class="n" style="color: #333;">characters</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1979
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<pre style="margin: 0;">+<span id="LC1979" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">include</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">IDs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1980
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<pre style="margin: 0;">+<span id="LC1980" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">23</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1981
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<pre style="margin: 0;">+<span id="LC1981" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1982
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<pre style="margin: 0;">+<span id="LC1982" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">missing</span><span class="p">\-</span><span class="n" style="color: #333;">var</span><span class="p">\-</span><span class="n" style="color: #333;">code</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="k" style="font-weight: 600;">string</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Change</span> <span class="n" style="color: #333;">unnamed</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">code</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="s1" style="color: #d14;">'.'</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1983
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<pre style="margin: 0;">+<span id="LC1983" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1984
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<pre style="margin: 0;">+<span id="LC1984" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">update</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1985
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<pre style="margin: 0;">+<span id="LC1985" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">chrcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">IDcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">skip</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">codes</span><span class="p">.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1986
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<pre style="margin: 0;">+<span id="LC1986" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1987
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<pre style="margin: 0;">+<span id="LC1987" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">update</span><span class="p">\-</span><span class="n" style="color: #333;">cm</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1988
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<pre style="margin: 0;">+<span id="LC1988" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">cmcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">IDcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">skip</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">centimorgan</span> <span class="n" style="color: #333;">positions</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1989
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<pre style="margin: 0;">+<span id="LC1989" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1990
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<pre style="margin: 0;">+<span id="LC1990" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">update</span><span class="p">\-</span><span class="n" style="color: #333;">map</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1991
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<pre style="margin: 0;">+<span id="LC1991" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">bpcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">IDcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">skip</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">bp</span> <span class="n" style="color: #333;">positions</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1992
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<pre style="margin: 0;">+<span id="LC1992" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1993
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<pre style="margin: 0;">+<span id="LC1993" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">update</span><span class="p">\-</span><span class="n" style="color: #333;">name</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">newcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">oldcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">skip</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">IDs</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1994
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<pre style="margin: 0;">+<span id="LC1994" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1995
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<pre style="margin: 0;">+<span id="LC1995" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">update</span><span class="p">\-</span><span class="n" style="color: #333;">alleles</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">fname</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">codes</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1996
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<pre style="margin: 0;">+<span id="LC1996" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1997
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<pre style="margin: 0;">+<span id="LC1997" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">allele1234</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'multichar'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Interpret</span><span class="p">/</span><span class="n" style="color: #333;">recode</span> <span class="n" style="color: #333;">A</span><span class="p">/</span><span class="n" style="color: #333;">C</span><span class="p">/</span><span class="n" style="color: #333;">G</span><span class="p">/</span><span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">alleles</span> <span class="k" style="font-weight: 600;">as</span> <span class="m" style="color: #099;">1</span><span class="p">/</span><span class="m" style="color: #099;">2</span><span class="p">/</span><span class="m" style="color: #099;">3</span><span class="p">/</span><span class="m" style="color: #099;">4.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1998
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<pre style="margin: 0;">+<span id="LC1998" class="line" lang="mosel"><span class="k" style="font-weight: 600;">With</span> <span class="s1" style="color: #d14;">'multichar'</span><span class="p">,</span> <span class="n" style="color: #333;">converts</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">A</span><span class="p">/</span><span class="n" style="color: #333;">C</span><span class="p">/</span><span class="n" style="color: #333;">G</span><span class="p">/</span><span class="n" style="color: #333;">Ts</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1999
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<pre style="margin: 0;">+<span id="LC1999" class="line" lang="mosel"><span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">1</span><span class="p">/</span><span class="m" style="color: #099;">2</span><span class="p">/</span><span class="m" style="color: #099;">3</span><span class="p">/</span><span class="m" style="color: #099;">4</span><span class="n" style="color: #333;">s</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2000
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<pre style="margin: 0;">+<span id="LC2000" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2001
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<pre style="margin: 0;">+<span id="LC2001" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">alleleACGT</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'multichar'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Reverse</span> <span class="k" style="font-weight: 600;">of</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">allele1234</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2002
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<pre style="margin: 0;">+<span id="LC2002" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2003
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<pre style="margin: 0;">+<span id="LC2003" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">update</span><span class="p">\-</span><span class="n" style="color: #333;">ids</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2004
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<pre style="margin: 0;">+<span id="LC2004" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">IDs</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2005
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<pre style="margin: 0;">+<span id="LC2005" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2006
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<pre style="margin: 0;">+<span id="LC2006" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">update</span><span class="p">\-</span><span class="n" style="color: #333;">parents</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">parental</span> <span class="n" style="color: #333;">IDs</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2007
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<pre style="margin: 0;">+<span id="LC2007" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2008
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<pre style="margin: 0;">+<span id="LC2008" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">update</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">sexes</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2009
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<pre style="margin: 0;">+<span id="LC2009" class="line" lang="mosel"><span class="n" style="color: #333;">Sex</span> <span class="p">(</span><span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">M</span> <span class="p">=</span> <span class="n" style="color: #333;">male</span><span class="p">,</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">F</span> <span class="p">=</span> <span class="n" style="color: #333;">female</span><span class="p">,</span> <span class="m" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2010
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<pre style="margin: 0;">+<span id="LC2010" class="line" lang="mosel"><span class="p">=</span> <span class="n" style="color: #333;">missing</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">loaded</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">column</span> <span class="n" style="color: #333;">n</span><span class="p">+</span><span class="m" style="color: #099;">2</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">n</span> <span class="n" style="color: #333;">is</span> <span class="m" style="color: #099;">1</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2011
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<pre style="margin: 0;">+<span id="LC2011" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2012
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<pre style="margin: 0;">+<span id="LC2012" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2013
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<pre style="margin: 0;">+<span id="LC2013" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Flip</span> <span class="n" style="color: #333;">alleles</span> <span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p"><\-></span><span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="n" style="color: #333;">C</span><span class="p"><\-></span><span class="n" style="color: #333;">G</span><span class="p">)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">SNP</span> <span class="n" style="color: #333;">IDs</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2014
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<pre style="margin: 0;">+<span id="LC2014" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2015
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<pre style="margin: 0;">+<span id="LC2015" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">subset</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">fn</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2016
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<pre style="margin: 0;">+<span id="LC2016" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Only</span> <span class="n" style="color: #333;">apply</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">subset</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2017
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<pre style="margin: 0;">+<span id="LC2017" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2018
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<pre style="margin: 0;">+<span id="LC2018" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">scan</span><span class="p">\-</span><span class="n" style="color: #333;">window</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">ct</span><span class="p">+</span><span class="m" style="color: #099;">1</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">scan</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">max</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ct</span> <span class="n" style="color: #333;">dist</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">def</span><span class="p">.</span> <span class="m" style="color: #099;">10</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2019
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<pre style="margin: 0;">+<span id="LC2019" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2020
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<pre style="margin: 0;">+<span id="LC2020" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">scan</span><span class="p">\-</span><span class="n" style="color: #333;">window</span><span class="p">\-</span><span class="n" style="color: #333;">kb</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">x</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">scan</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">max</span> <span class="n" style="color: #333;">kb</span> <span class="n" style="color: #333;">distance</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">1000</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2021
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<pre style="margin: 0;">+<span id="LC2021" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2022
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<pre style="margin: 0;">+<span id="LC2022" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">scan</span><span class="p">\-</span><span class="n" style="color: #333;">threshold</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">x</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">flip</span><span class="p">\-</span><span class="n" style="color: #333;">scan</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">min</span> <span class="n" style="color: #333;">correlation</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.5</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2023
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<pre style="margin: 0;">+<span id="LC2023" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2024
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<pre style="margin: 0;">+<span id="LC2024" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">keep</span><span class="p">\-</span><span class="n" style="color: #333;">allele</span><span class="p">\-</span><span class="n" style="color: #333;">order</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2025
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<pre style="margin: 0;">+<span id="LC2025" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Keep</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">defined</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="p">.</span><span class="n" style="color: #333;">bim</span> <span class="n" style="color: #333;">file</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2026
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<pre style="margin: 0;">+<span id="LC2026" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2027
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<pre style="margin: 0;">+<span id="LC2027" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">real</span><span class="p">\-</span><span class="n" style="color: #333;">ref</span><span class="p">\-</span><span class="n" style="color: #333;">alleles</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2028
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<pre style="margin: 0;">+<span id="LC2028" class="line" lang="mosel"><span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">forcing</span> <span class="n" style="color: #333;">A2</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">major</span> <span class="n" style="color: #333;">allele</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2029
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<pre style="margin: 0;">+<span id="LC2029" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">real</span><span class="p">\-</span><span class="n" style="color: #333;">ref</span><span class="p">\-</span><span class="n" style="color: #333;">alleles</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">removes</span> <span class="s1" style="color: #d14;">'PR'</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">INFO</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="mosel"><span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">emitted</span> <span class="n" style="color: #333;">by</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">recode</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">vcf</span><span class="p">{,\-</span><span class="n" style="color: #333;">fid</span><span class="p">,\-</span><span class="n" style="color: #333;">iid</span><span class="p">}.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2031
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<pre style="margin: 0;">+<span id="LC2031" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2032
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<pre style="margin: 0;">+<span id="LC2032" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">a1</span><span class="p">\-</span><span class="n" style="color: #333;">allele</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">f</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">a1col</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">IDcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">skip</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Force</span> <span class="n" style="color: #333;">alleles</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">A1</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2033
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<pre style="margin: 0;">+<span id="LC2033" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2034
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<pre style="margin: 0;">+<span id="LC2034" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">a2</span><span class="p">\-</span><span class="n" style="color: #333;">allele</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">a2col</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">IDcol</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">skip</span><span class="p">]</span> <span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2035
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<pre style="margin: 0;">+<span id="LC2035" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2036
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<pre style="margin: 0;">+<span id="LC2036" class="line" lang="mosel"><span class="n" style="color: #333;">Force</span> <span class="n" style="color: #333;">alleles</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">A2</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2037
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<pre style="margin: 0;">+<span id="LC2037" class="line" lang="mosel"><span class="p">(</span><span class="s2" style="color: #d14;">"\-\-a2\-allele <VCF filename> 4 3 '#'"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2038
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<pre style="margin: 0;">+<span id="LC2038" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2039
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<pre style="margin: 0;">+<span id="LC2039" class="line" lang="mosel"><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">scrapes</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">allele</span> <span class="n" style="color: #333;">assignments</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">VCF</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">especially</span></span>
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2040
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<pre style="margin: 0;">+<span id="LC2040" class="line" lang="mosel"><span class="n" style="color: #333;">useful</span><span class="p">.)</span></span>
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2041
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<pre style="margin: 0;">+<span id="LC2041" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2042
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<pre style="margin: 0;">+<span id="LC2042" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">indiv</span><span class="p">\-</span><span class="n" style="color: #333;">sort</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">m</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">f</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">FID</span><span class="p">/</span><span class="n" style="color: #333;">IID</span> <span class="n" style="color: #333;">sort</span> <span class="n" style="color: #333;">order</span><span class="p">.</span></span>
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2043
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<pre style="margin: 0;">+<span id="LC2043" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">four</span> <span class="n" style="color: #333;">modes</span></span>
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2044
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<pre style="margin: 0;">+<span id="LC2044" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">supported</span><span class="p">:</span></span>
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2045
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<pre style="margin: 0;">+<span id="LC2045" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'none'</span><span class="p">/</span><span class="s1" style="color: #d14;">'0'</span> <span class="n" style="color: #333;">keeps</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">were</span></span>
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2046
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<pre style="margin: 0;">+<span id="LC2046" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2047
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<pre style="margin: 0;">+<span id="LC2047" class="line" lang="mosel"><span class="n" style="color: #333;">loaded</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2048
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<pre style="margin: 0;">+<span id="LC2048" class="line" lang="mosel"><span class="n" style="color: #333;">Default</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">non</span><span class="p">\-</span><span class="n" style="color: #333;">merge</span> <span class="n" style="color: #333;">operations</span><span class="p">.</span></span>
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2049
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<pre style="margin: 0;">+<span id="LC2049" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2050
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<pre style="margin: 0;">+<span id="LC2050" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'natural'</span><span class="p">/</span><span class="s1" style="color: #d14;">'n'</span> <span class="n" style="color: #333;">invokes</span> <span class="s1" style="color: #d14;">'natural sort'</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2051
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<pre style="margin: 0;">+<span id="LC2051" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'id2'</span> <span class="p"><</span> <span class="s1" style="color: #d14;">'ID3'</span> <span class="p"><</span> <span class="s1" style="color: #d14;">'id10'</span><span class="p">.</span> <span class="n" style="color: #333;">Default</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">merging</span><span class="p">.</span></span>
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2052
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<pre style="margin: 0;">+<span id="LC2052" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2053
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<pre style="margin: 0;">+<span id="LC2053" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'ascii'</span><span class="p">/</span><span class="s1" style="color: #d14;">'a'</span> <span class="n" style="color: #333;">sorts</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ASCII</span> <span class="n" style="color: #333;">order</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span></span>
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2054
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<pre style="margin: 0;">+<span id="LC2054" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'ID3'</span> <span class="p"><</span> <span class="s1" style="color: #d14;">'id10'</span> <span class="p"><</span> <span class="s1" style="color: #d14;">'id2'</span><span class="p">.</span></span>
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2055
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<pre style="margin: 0;">+<span id="LC2055" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2056
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<pre style="margin: 0;">+<span id="LC2056" class="line" lang="mosel"><span class="p">*</span> <span class="s1" style="color: #d14;">'file'</span><span class="p">/</span><span class="s1" style="color: #d14;">'f'</span> <span class="k" style="font-weight: 600;">uses</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">order</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">file</span> <span class="p">(</span><span class="n" style="color: #333;">named</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2057
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<pre style="margin: 0;">+<span id="LC2057" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">second</span> <span class="n" style="color: #333;">parameter</span><span class="p">).</span></span>
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2058
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<pre style="margin: 0;">+<span id="LC2058" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2059
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<pre style="margin: 0;">+<span id="LC2059" class="line" lang="mosel"><span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">now</span><span class="p">,</span> <span class="n" style="color: #333;">only</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">bmerge</span><span class="p">/\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\-</span><span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">and</span></span>
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2060
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<pre style="margin: 0;">+<span id="LC2060" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">bed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">make</span><span class="p">\-</span><span class="n" style="color: #333;">just</span><span class="p">\-</span><span class="n" style="color: #333;">fam</span> <span class="n" style="color: #333;">respect</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">flag</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2061
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<pre style="margin: 0;">+<span id="LC2061" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2062
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<pre style="margin: 0;">+<span id="LC2062" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">with</span><span class="p">\-</span><span class="n" style="color: #333;">phenotype</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-parents'</span><span class="p">]</span> <span class="p">[{</span><span class="n" style="color: #333;">no</span><span class="p">\-</span><span class="n" style="color: #333;">sex</span> <span class="p">|</span> <span class="n" style="color: #333;">female</span><span class="p">\-</span><span class="m" style="color: #099;">2</span><span class="p">}]</span> <span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2063
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<pre style="margin: 0;">+<span id="LC2063" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2064
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<pre style="margin: 0;">+<span id="LC2064" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">info</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="p">.</span><span class="n" style="color: #333;">cov</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2065
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<pre style="margin: 0;">+<span id="LC2065" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2066
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<pre style="margin: 0;">+<span id="LC2066" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">dummy</span><span class="p">\-</span><span class="n" style="color: #333;">coding</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">N</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'no\-round'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Split</span> <span class="n" style="color: #333;">categorical</span> <span class="n" style="color: #333;">variables</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="n" style="color: #333;">categories</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2067
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<pre style="margin: 0;">+<span id="LC2067" class="line" lang="mosel"><span class="m" style="color: #099;">2</span> <span class="p"><</span> <span class="n" style="color: #333;">n</span> <span class="p"><=</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">N</span> <span class="n" style="color: #333;">is</span> <span class="m" style="color: #099;">49</span><span class="p">)</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">n</span><span class="p">\-</span><span class="m" style="color: #099;">1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2068
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<pre style="margin: 0;">+<span id="LC2068" class="line" lang="mosel"><span class="n" style="color: #333;">binary</span> <span class="n" style="color: #333;">dummy</span> <span class="n" style="color: #333;">variables</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">writing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2069
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<pre style="margin: 0;">+<span id="LC2069" class="line" lang="mosel"><span class="n" style="color: #333;">covariate</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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2070
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<pre style="margin: 0;">+<span id="LC2070" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2071
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<pre style="margin: 0;">+<span id="LC2071" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\-</span><span class="n" style="color: #333;">mode</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2072
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<pre style="margin: 0;">+<span id="LC2072" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Adjust</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-[</span><span class="n" style="color: #333;">b</span><span class="p">]</span><span class="n" style="color: #333;">merge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\-</span><span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">behavior</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2073
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<pre style="margin: 0;">+<span id="LC2073" class="line" lang="mosel"><span class="n" style="color: #333;">numeric</span> <span class="n" style="color: #333;">code</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2074
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<pre style="margin: 0;">+<span id="LC2074" class="line" lang="mosel"><span class="m" style="color: #099;">1</span> <span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">)</span> <span class="p">=</span> <span class="n" style="color: #333;">ignore</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">calls</span><span class="p">,</span> <span class="n" style="color: #333;">otherwise</span> <span class="n" style="color: #333;">difference</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2075
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<pre style="margin: 0;">+<span id="LC2075" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2076
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<pre style="margin: 0;">+<span id="LC2076" class="line" lang="mosel"><span class="p">\-></span> <span class="n" style="color: #333;">missing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2077
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<pre style="margin: 0;">+<span id="LC2077" class="line" lang="mosel"><span class="m" style="color: #099;">2</span> <span class="p">=</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">overwrite</span> <span class="n" style="color: #333;">originally</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">calls</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2078
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<pre style="margin: 0;">+<span id="LC2078" class="line" lang="mosel"><span class="m" style="color: #099;">3</span> <span class="p">=</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">overwrite</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">nonmissing</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">file</span></span>
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2079
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<pre style="margin: 0;">+<span id="LC2079" class="line" lang="mosel"><span class="m" style="color: #099;">4</span><span class="p">/</span><span class="m" style="color: #099;">5</span> <span class="p">=</span> <span class="n" style="color: #333;">never</span> <span class="n" style="color: #333;">overwrite</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">always</span> <span class="n" style="color: #333;">overwrite</span><span class="p">,</span> <span class="n" style="color: #333;">respectively</span></span>
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2080
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<pre style="margin: 0;">+<span id="LC2080" class="line" lang="mosel"><span class="m" style="color: #099;">6</span> <span class="p">=</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">mismatching</span> <span class="n" style="color: #333;">calls</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">merging</span></span>
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2081
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<pre style="margin: 0;">+<span id="LC2081" class="line" lang="mosel"><span class="m" style="color: #099;">7</span> <span class="p">=</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">mismatching</span> <span class="n" style="color: #333;">nonmissing</span> <span class="n" style="color: #333;">calls</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">merging</span></span>
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2082
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<pre style="margin: 0;">+<span id="LC2082" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2083
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<pre style="margin: 0;">+<span id="LC2083" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\-</span><span class="n" style="color: #333;">equal</span><span class="p">\-</span><span class="n" style="color: #333;">pos</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2084
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<pre style="margin: 0;">+<span id="LC2084" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">With</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">/\-\-</span><span class="n" style="color: #333;">bmerge</span><span class="p">/\-\-</span><span class="n" style="color: #333;">merge</span><span class="p">\-</span><span class="k" style="font-weight: 600;">list</span><span class="p">,</span> <span class="n" style="color: #333;">merge</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2085
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<pre style="margin: 0;">+<span id="LC2085" class="line" lang="mosel"><span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">names</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">identical</span> <span class="n" style="color: #333;">positions</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Exception</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2086
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<pre style="margin: 0;">+<span id="LC2086" class="line" lang="mosel"><span class="n" style="color: #333;">same</span><span class="p">\-</span><span class="n" style="color: #333;">position</span> <span class="n" style="color: #333;">chromosome</span> <span class="n" style="color: #333;">code</span> <span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">variants</span> <span class="n" style="color: #333;">aren</span><span class="s1" style="color: #d14;">'t merged.)</span></span>
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2087
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<pre style="margin: 0;">+<span id="LC2087" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2088
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<pre style="margin: 0;">+<span id="LC2088" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-mendel\-duos\fR</span></span>
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2089
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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Make Mendel error checks consider samples with only one</span></span>
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2090
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<pre style="margin: 0;">+<span id="LC2090" class="line" lang="mosel"><span class="s1" style="color: #d14;">parent in the dataset.</span></span>
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2091
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<pre style="margin: 0;">+<span id="LC2091" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2092
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<pre style="margin: 0;">+<span id="LC2092" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-mendel\-multigen\fR</span></span>
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2093
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Make Mendel error checks consider (great\-)grandparental</span></span>
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2094
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="mosel"><span class="s1" style="color: #d14;">genotypes when parental genotype data is missing.</span></span>
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2095
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<pre style="margin: 0;">+<span id="LC2095" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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2096
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<pre style="margin: 0;">+<span id="LC2096" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ld\-window\fR <ct+1> : Set \fB\-\-r\fR/\-\-r2 max variant ct pairwise distance (usu. 10).</span></span>
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2097
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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2098
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ld\-window\-kb\fR <x> : Set \fB\-\-r\fR/\-\-r2 max kb pairwise distance (usually 1000).</span></span>
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2099
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<pre style="margin: 0;">+<span id="LC2099" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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2100
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<pre style="margin: 0;">+<span id="LC2100" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ld\-window\-cm\fR <x> : Set \fB\-\-r\fR/\-\-r2 max centimorgan pairwise distance.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2101
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<pre style="margin: 0;">+<span id="LC2101" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2102
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<pre style="margin: 0;">+<span id="LC2102" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ld\-window\-r2\fR <x> : Set threshold for \fB\-\-r2\fR report inclusion (usually 0.2).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2103
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<pre style="margin: 0;">+<span id="LC2103" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2104
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<pre style="margin: 0;">+<span id="LC2104" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ld\-snp\fR <var ID></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2105
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<pre style="margin: 0;">+<span id="LC2105" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set first variant in all \fB\-\-r\fR/\-\-r2 pairs.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2106
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<pre style="margin: 0;">+<span id="LC2106" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2107
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<pre style="margin: 0;">+<span id="LC2107" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ld\-snps\fR <vID...> : Restrict first \fB\-\-r\fR/\-\-r2 variant to the given ranges.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2108
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<pre style="margin: 0;">+<span id="LC2108" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2109
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<pre style="margin: 0;">+<span id="LC2109" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ld\-snp\-list\fR <f></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2110
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<pre style="margin: 0;">+<span id="LC2110" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Restrict first \fB\-\-r\fR/\-\-r2 var. to those named in the file.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2111
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<pre style="margin: 0;">+<span id="LC2111" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2112
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<pre style="margin: 0;">+<span id="LC2112" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-list\-all\fR</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2113
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<pre style="margin: 0;">+<span id="LC2113" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Generate the '</span><span class="n" style="color: #333;">all</span><span class="s1" style="color: #d14;">' mode report when using \fB\-\-show\-tags\fR in</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2114
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<pre style="margin: 0;">+<span id="LC2114" class="line" lang="mosel"><span class="s1" style="color: #d14;">file mode.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2115
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<pre style="margin: 0;">+<span id="LC2115" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2116
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<pre style="margin: 0;">+<span id="LC2116" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tag\-kb\fR <kbs></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2117
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<pre style="margin: 0;">+<span id="LC2117" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set \fB\-\-show\-tags\fR max tag kb distance (default 250).</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2118
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<pre style="margin: 0;">+<span id="LC2118" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2119
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<pre style="margin: 0;">+<span id="LC2119" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tag\-r2\fR <val></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2120
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<pre style="margin: 0;">+<span id="LC2120" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set \fB\-\-show\-tags\fR min tag r\-squared (default 0.8)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2121
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<pre style="margin: 0;">+<span id="LC2121" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2122
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<pre style="margin: 0;">+<span id="LC2122" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tag\-mode2\fR</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2123
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<pre style="margin: 0;">+<span id="LC2123" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Use two\-column \fB\-\-show\-tags\fR (file mode) I/O format.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2124
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<pre style="margin: 0;">+<span id="LC2124" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2125
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<pre style="margin: 0;">+<span id="LC2125" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ld\-xchr\fR <code></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2126
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<pre style="margin: 0;">+<span id="LC2126" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set chrX model for \fB\-\-indep[\-pairwise]\fR, \fB\-\-r\fR/\-\-r2,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2127
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<pre style="margin: 0;">+<span id="LC2127" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-flip\-scan\fR, and \fB\-\-show\-tags\fR.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2128
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<pre style="margin: 0;">+<span id="LC2128" class="line" lang="mosel"><span class="s1" style="color: #d14;">1 (default) = males coded 0/1, females 0/1/2 (A1 dosage)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2129
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<pre style="margin: 0;">+<span id="LC2129" class="line" lang="mosel"><span class="s1" style="color: #d14;">2 = males coded 0/2</span></span>
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2130
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<pre style="margin: 0;">+<span id="LC2130" class="line" lang="mosel"><span class="s1" style="color: #d14;">3 = males coded 0/2, but females given double weighting</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2131
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<pre style="margin: 0;">+<span id="LC2131" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2132
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<pre style="margin: 0;">+<span id="LC2132" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-blocks\-max\-kb\fR <kbs></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2133
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<pre style="margin: 0;">+<span id="LC2133" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set \fB\-\-blocks\fR maximum haploblock span (def. 200).</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2134
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<pre style="margin: 0;">+<span id="LC2134" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2135
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<pre style="margin: 0;">+<span id="LC2135" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-blocks\-min\-maf\fR <cutoff></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2136
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<pre style="margin: 0;">+<span id="LC2136" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Adjust \fB\-\-blocks\fR MAF minimum (default 0.05).</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2137
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<pre style="margin: 0;">+<span id="LC2137" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2138
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<pre style="margin: 0;">+<span id="LC2138" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-blocks\-strong\-lowci\fR <x></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2139
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<pre style="margin: 0;">+<span id="LC2139" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set \fB\-\-blocks\fR "strong LD" CI thresholds (defaults</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2140
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<pre style="margin: 0;">+<span id="LC2140" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2141
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<pre style="margin: 0;">+<span id="LC2141" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-blocks\-strong\-highci\fR <x></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2142
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<pre style="margin: 0;">+<span id="LC2142" class="line" lang="mosel"><span class="s1" style="color: #d14;">0.70 and 0.98).</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2143
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<pre style="margin: 0;">+<span id="LC2143" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2144
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<pre style="margin: 0;">+<span id="LC2144" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-blocks\-recomb\-highci\fR <x> : Set '</span><span class="n" style="color: #333;">recombination</span><span class="s1" style="color: #d14;">' CI threshold (default 0.90).</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2145
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<pre style="margin: 0;">+<span id="LC2145" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2146
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<pre style="margin: 0;">+<span id="LC2146" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-blocks\-inform\-frac\fR <x></span></span>
</pre>
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2147
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<pre style="margin: 0;">+<span id="LC2147" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Force haploblock <strong LD pairs>:<total</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2148
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<pre style="margin: 0;">+<span id="LC2148" class="line" lang="mosel"><span class="s1" style="color: #d14;">informative pairs> ratios to be larger than this</span></span>
</pre>
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2149
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<pre style="margin: 0;">+<span id="LC2149" class="line" lang="mosel"><span class="s1" style="color: #d14;">value (default 0.95).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2150
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<pre style="margin: 0;">+<span id="LC2150" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2151
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-distance\-wts\fR exp=<x></span></span>
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2152
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<pre style="margin: 0;">+<span id="LC2152" class="line" lang="mosel"><span class="s1" style="color: #d14;">: When computing genomic distances, assign each</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2153
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<pre style="margin: 0;">+<span id="LC2153" class="line" lang="mosel"><span class="s1" style="color: #d14;">variant a weight of (2q(1\-q))^{\-x}, where q</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2154
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<pre style="margin: 0;">+<span id="LC2154" class="line" lang="mosel"><span class="s1" style="color: #d14;">is the loaded or inferred MAF.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2155
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<pre style="margin: 0;">+<span id="LC2155" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2156
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<pre style="margin: 0;">+<span id="LC2156" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-read\-dists\fR <dist file> [id file] : Load a triangular binary distance matrix</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2157
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<pre style="margin: 0;">+<span id="LC2157" class="line" lang="mosel"><span class="s1" style="color: #d14;">instead of recalculating from scratch.</span></span>
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2158
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<pre style="margin: 0;">+<span id="LC2158" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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2159
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<pre style="margin: 0;">+<span id="LC2159" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ppc\-gap\fR <val></span></span>
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2160
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<pre style="margin: 0;">+<span id="LC2160" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Minimum number of base pairs, in thousands, between</span></span>
</pre>
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2161
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<pre style="margin: 0;">+<span id="LC2161" class="line" lang="mosel"><span class="s1" style="color: #d14;">informative pairs of markers used in \fB\-\-genome\fR PPC test.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2162
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<pre style="margin: 0;">+<span id="LC2162" class="line" lang="mosel"><span class="s1" style="color: #d14;">500 if unspecified.</span></span>
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2163
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<pre style="margin: 0;">+<span id="LC2163" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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2164
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<pre style="margin: 0;">+<span id="LC2164" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-min\fR <cutoff></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2165
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<pre style="margin: 0;">+<span id="LC2165" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify minimum PI_HAT for inclusion in \fB\-\-genome\fR report.</span></span>
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2166
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<pre style="margin: 0;">+<span id="LC2166" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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2167
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<pre style="margin: 0;">+<span id="LC2167" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-max\fR <cutoff></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2168
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<pre style="margin: 0;">+<span id="LC2168" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify maximum PI_HAT for inclusion in \fB\-\-genome\fR report.</span></span>
</pre>
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2169
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<pre style="margin: 0;">+<span id="LC2169" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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2170
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<pre style="margin: 0;">+<span id="LC2170" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-homozyg\-match\fR <> : Set minimum concordance across jointly homozygous</span></span>
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2171
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<pre style="margin: 0;">+<span id="LC2171" class="line" lang="mosel"><span class="s1" style="color: #d14;">variants for a pairwise allelic match to be declared.</span></span>
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2172
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<pre style="margin: 0;">+<span id="LC2172" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2173
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<pre style="margin: 0;">+<span id="LC2173" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-pool\-size\fR <ct></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2174
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<pre style="margin: 0;">+<span id="LC2174" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set minimum size of pools in "\-\-homozyg group" report.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2175
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<pre style="margin: 0;">+<span id="LC2175" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2176
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<pre style="margin: 0;">+<span id="LC2176" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-read\-genome\fR <fn> : Load \fB\-\-genome\fR report for \fB\-\-cluster\fR/\-\-neighbour, instead</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2177
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<pre style="margin: 0;">+<span id="LC2177" class="line" lang="mosel"><span class="s1" style="color: #d14;">of recalculating IBS and PPC test p\-values from scratch.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2178
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<pre style="margin: 0;">+<span id="LC2178" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2179
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<pre style="margin: 0;">+<span id="LC2179" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ppc\fR <p\-val></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2180
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<pre style="margin: 0;">+<span id="LC2180" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify minimum PPC test p\-value within a cluster.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2181
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<pre style="margin: 0;">+<span id="LC2181" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2182
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<pre style="margin: 0;">+<span id="LC2182" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-mc\fR <max size></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2183
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<pre style="margin: 0;">+<span id="LC2183" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify maximum cluster size.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2184
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<pre style="margin: 0;">+<span id="LC2184" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2185
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<pre style="margin: 0;">+<span id="LC2185" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-mcc\fR <c1> <c2></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2186
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<pre style="margin: 0;">+<span id="LC2186" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify maximum case and control counts per cluster.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2187
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<pre style="margin: 0;">+<span id="LC2187" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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2188
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<pre style="margin: 0;">+<span id="LC2188" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-K\fR <min count></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2189
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<pre style="margin: 0;">+<span id="LC2189" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify minimum cluster count.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2190
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<pre style="margin: 0;">+<span id="LC2190" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2191
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<pre style="margin: 0;">+<span id="LC2191" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ibm\fR <val></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2192
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<pre style="margin: 0;">+<span id="LC2192" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Specify minimum identity\-by\-missingness.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2193
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<pre style="margin: 0;">+<span id="LC2193" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2194
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<pre style="margin: 0;">+<span id="LC2194" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-match\fR <f> [mv] : Use covariate values to restrict clustering.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2195
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<pre style="margin: 0;">+<span id="LC2195" class="line" lang="mosel"><span class="s1" style="color: #d14;">Without</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2196
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<pre style="margin: 0;">+<span id="LC2196" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-match\-type\fR, two samples can only be in the same cluster</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2197
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<pre style="margin: 0;">+<span id="LC2197" class="line" lang="mosel"><span class="s1" style="color: #d14;">if all covariates match. The optional second parameter</span></span>
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2198
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<pre style="margin: 0;">+<span id="LC2198" class="line" lang="mosel"><span class="s1" style="color: #d14;">specifies a covariate value to treat as missing.</span></span>
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2199
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<pre style="margin: 0;">+<span id="LC2199" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2200
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<pre style="margin: 0;">+<span id="LC2200" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-match\-type\fR <f> : Refine interpretation of \fB\-\-match\fR file.</span></span>
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2201
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<pre style="margin: 0;">+<span id="LC2201" class="line" lang="mosel"><span class="s1" style="color: #d14;">The \fB\-\-match\-type\fR</span></span>
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2202
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<pre style="margin: 0;">+<span id="LC2202" class="line" lang="mosel"><span class="s1" style="color: #d14;">file is expected to be a single line with as many entries</span></span>
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2203
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<pre style="margin: 0;">+<span id="LC2203" class="line" lang="mosel"><span class="s1" style="color: #d14;">as the \fB\-\-match\fR file has covariates; '</span><span class="m" style="color: #099;">0</span><span class="s1" style="color: #d14;">' entries specify</span></span>
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2204
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<pre style="margin: 0;">+<span id="LC2204" class="line" lang="mosel"><span class="s1" style="color: #d14;">"negative matches" (i.e. samples with equal covariate</span></span>
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2205
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<pre style="margin: 0;">+<span id="LC2205" class="line" lang="mosel"><span class="s1" style="color: #d14;">values cannot be in the same cluster), '</span><span class="m" style="color: #099;">1</span><span class="s1" style="color: #d14;">' entries specify</span></span>
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2206
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<pre style="margin: 0;">+<span id="LC2206" class="line" lang="mosel"><span class="s1" style="color: #d14;">"positive matches" (default), and '</span><span class="p">\-</span><span class="m" style="color: #099;">1</span><span class="s1" style="color: #d14;">' causes the</span></span>
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2207
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<pre style="margin: 0;">+<span id="LC2207" class="line" lang="mosel"><span class="s1" style="color: #d14;">corresponding covariate to be ignored.</span></span>
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2208
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<pre style="margin: 0;">+<span id="LC2208" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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2209
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<pre style="margin: 0;">+<span id="LC2209" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-qmatch\fR <f> [m] : Force all members of a cluster to have similar</span></span>
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2210
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<pre style="margin: 0;">+<span id="LC2210" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2211
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<pre style="margin: 0;">+<span id="LC2211" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-qt\fR <fname></span></span>
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2212
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<pre style="margin: 0;">+<span id="LC2212" class="line" lang="mosel"><span class="s1" style="color: #d14;">quantitative covariate values. The \fB\-\-qmatch\fR file contains</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2213
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<pre style="margin: 0;">+<span id="LC2213" class="line" lang="mosel"><span class="s1" style="color: #d14;">the covariate values, while the \fB\-\-qt\fR file is a list of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2214
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<pre style="margin: 0;">+<span id="LC2214" class="line" lang="mosel"><span class="s1" style="color: #d14;">nonnegative tolerances (and '</span><span class="p">\-</span><span class="m" style="color: #099;">1</span><span class="s1" style="color: #d14;">'s marking covariates to</span></span>
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2215
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<pre style="margin: 0;">+<span id="LC2215" class="line" lang="mosel"><span class="s1" style="color: #d14;">skip).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2216
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<pre style="margin: 0;">+<span id="LC2216" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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2217
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<pre style="margin: 0;">+<span id="LC2217" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-pca\-cluster\-names\fR <...> : These can be used individually or in combination</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2218
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<pre style="margin: 0;">+<span id="LC2218" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2219
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<pre style="margin: 0;">+<span id="LC2219" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-pca\-clusters\fR <fname></span></span>
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2220
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<pre style="margin: 0;">+<span id="LC2220" class="line" lang="mosel"><span class="s1" style="color: #d14;">to define a list of clusters to use in the basic</span></span>
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2221
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<pre style="margin: 0;">+<span id="LC2221" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-pca\fR computation. (\fB\-\-pca\-cluster\-names\fR expects</span></span>
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2222
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<pre style="margin: 0;">+<span id="LC2222" class="line" lang="mosel"><span class="s1" style="color: #d14;">a space\-delimited sequence of cluster names,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2223
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<pre style="margin: 0;">+<span id="LC2223" class="line" lang="mosel"><span class="s1" style="color: #d14;">while \fB\-\-pca\-clusters\fR expects a file with one</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2224
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<pre style="margin: 0;">+<span id="LC2224" class="line" lang="mosel"><span class="s1" style="color: #d14;">cluster name per line.) All samples outside</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2225
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<pre style="margin: 0;">+<span id="LC2225" class="line" lang="mosel"><span class="s1" style="color: #d14;">those clusters will then be projected on to the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2226
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<pre style="margin: 0;">+<span id="LC2226" class="line" lang="mosel"><span class="s1" style="color: #d14;">calculated PCs.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2227
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<pre style="margin: 0;">+<span id="LC2227" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2228
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<pre style="margin: 0;">+<span id="LC2228" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-mds\-plot\fR <dims> ['</span><span class="n" style="color: #333;">by</span><span class="p">\-</span><span class="n" style="color: #333;">cluster</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">eigendecomp</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">eigvals</span><span class="s1" style="color: #d14;">'] :</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2229
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<pre style="margin: 0;">+<span id="LC2229" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2230
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<pre style="margin: 0;">+<span id="LC2230" class="line" lang="mosel"><span class="s1" style="color: #d14;">Multidimensional scaling analysis.</span></span>
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2231
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<pre style="margin: 0;">+<span id="LC2231" class="line" lang="mosel"><span class="s1" style="color: #d14;">Requires \fB\-\-cluster\fR.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2232
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<pre style="margin: 0;">+<span id="LC2232" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2233
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<pre style="margin: 0;">+<span id="LC2233" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-cell\fR <thresh></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2234
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<pre style="margin: 0;">+<span id="LC2234" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Skip some \fB\-\-model\fR tests when a contingency table entry is</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2235
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<pre style="margin: 0;">+<span id="LC2235" class="line" lang="mosel"><span class="s1" style="color: #d14;">smaller than the given threshold.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2236
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<pre style="margin: 0;">+<span id="LC2236" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2237
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<pre style="margin: 0;">+<span id="LC2237" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-condition\fR <var ID> [{dominant | recessive}] : Add one variant as a \fB\-\-linear\fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2238
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<pre style="margin: 0;">+<span id="LC2238" class="line" lang="mosel"><span class="s1" style="color: #d14;">or \fB\-\-logistic\fR covariate.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2239
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<pre style="margin: 0;">+<span id="LC2239" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2240
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<pre style="margin: 0;">+<span id="LC2240" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-condition\-list\fR <f> [{dominant | recessive}] : Add variants named in the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2241
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<pre style="margin: 0;">+<span id="LC2241" class="line" lang="mosel"><span class="s1" style="color: #d14;">file as \fB\-\-linear\fR/\-\-logistic</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2242
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<pre style="margin: 0;">+<span id="LC2242" class="line" lang="mosel"><span class="s1" style="color: #d14;">covariates.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2243
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<pre style="margin: 0;">+<span id="LC2243" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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2244
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<pre style="margin: 0;">+<span id="LC2244" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-parameters\fR <...></span></span>
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2245
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<pre style="margin: 0;">+<span id="LC2245" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Include only the given covariates/interactions in the</span></span>
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2246
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<pre style="margin: 0;">+<span id="LC2246" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-linear\fR/\-\-logistic models, identified by a list of</span></span>
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2247
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<pre style="margin: 0;">+<span id="LC2247" class="line" lang="mosel"><span class="s1" style="color: #d14;">1\-based indices and/or ranges of them.</span></span>
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2248
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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2249
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<pre style="margin: 0;">+<span id="LC2249" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-tests\fR <all> [...] : Perform a (joint) test on the specified term(s) in the</span></span>
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2250
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<pre style="margin: 0;">+<span id="LC2250" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-linear\fR/\-\-logistic model, identified by 1\-based</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2251
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<pre style="margin: 0;">+<span id="LC2251" class="line" lang="mosel"><span class="s1" style="color: #d14;">indices and/or ranges of them. If permutation was</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2252
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<pre style="margin: 0;">+<span id="LC2252" class="line" lang="mosel"><span class="s1" style="color: #d14;">requested, it is based on this test.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2253
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<pre style="margin: 0;">+<span id="LC2253" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Note that, when \fB\-\-parameters\fR is also present, the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2254
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<pre style="margin: 0;">+<span id="LC2254" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2255
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<pre style="margin: 0;">+<span id="LC2255" class="line" lang="mosel"><span class="s1" style="color: #d14;">indices refer to the terms remaining AFTER pruning by</span></span>
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2256
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<pre style="margin: 0;">+<span id="LC2256" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-parameters\fR.</span></span>
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2257
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<pre style="margin: 0;">+<span id="LC2257" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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2258
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<pre style="margin: 0;">+<span id="LC2258" class="line" lang="mosel"><span class="s1" style="color: #d14;">* You can use "\-\-tests all" to include all terms.</span></span>
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2259
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<pre style="margin: 0;">+<span id="LC2259" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2260
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<pre style="margin: 0;">+<span id="LC2260" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-vif\fR <max VIF></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2261
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<pre style="margin: 0;">+<span id="LC2261" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set VIF threshold for \fB\-\-linear\fR multicollinearity check</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2262
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<pre style="margin: 0;">+<span id="LC2262" class="line" lang="mosel"><span class="s1" style="color: #d14;">(default 50).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2263
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<pre style="margin: 0;">+<span id="LC2263" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
</pre>
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2264
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<pre style="margin: 0;">+<span id="LC2264" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-xchr\-model\fR <code> : Set the X chromosome \fB\-\-linear\fR/\-\-logistic model.</span></span>
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2265
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<pre style="margin: 0;">+<span id="LC2265" class="line" lang="mosel"><span class="s1" style="color: #d14;">0 = skip sex and haploid chromosomes</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2266
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<pre style="margin: 0;">+<span id="LC2266" class="line" lang="mosel"><span class="s1" style="color: #d14;">1 (default) = add sex as a covariate on X chromosome</span></span>
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2267
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<pre style="margin: 0;">+<span id="LC2267" class="line" lang="mosel"><span class="s1" style="color: #d14;">2 = code male genotypes 0/2 instead of 0/1</span></span>
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2268
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<pre style="margin: 0;">+<span id="LC2268" class="line" lang="mosel"><span class="s1" style="color: #d14;">3 = test for interaction between genotype and sex</span></span>
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2269
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<pre style="margin: 0;">+<span id="LC2269" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2270
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<pre style="margin: 0;">+<span id="LC2270" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-lasso\-select\-covars\fR [cov(s)...] : Subject some or all covariates to LASSO</span></span>
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2271
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<pre style="margin: 0;">+<span id="LC2271" class="line" lang="mosel"><span class="s1" style="color: #d14;">model selection.</span></span>
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2272
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<pre style="margin: 0;">+<span id="LC2272" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2273
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<pre style="margin: 0;">+<span id="LC2273" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-adjust\fR ['</span><span class="n" style="color: #333;">gc</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">log10</span><span class="s1" style="color: #d14;">'] ['</span><span class="n" style="color: #333;">qq</span><span class="p">\-</span><span class="n" style="color: #333;">plot</span><span class="s1" style="color: #d14;">'] : Report some multiple\-testing</span></span>
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2274
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<pre style="margin: 0;">+<span id="LC2274" class="line" lang="mosel"><span class="s1" style="color: #d14;">corrections.</span></span>
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2275
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<pre style="margin: 0;">+<span id="LC2275" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2276
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<pre style="margin: 0;">+<span id="LC2276" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-lambda\fR <val></span></span>
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2277
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<pre style="margin: 0;">+<span id="LC2277" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Set genomic control lambda for \fB\-\-adjust\fR.</span></span>
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2278
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<pre style="margin: 0;">+<span id="LC2278" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2279
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<pre style="margin: 0;">+<span id="LC2279" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-ci\fR <size></span></span>
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2280
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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Report confidence intervals for odds ratios.</span></span>
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2281
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<pre style="margin: 0;">+<span id="LC2281" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2282
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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-pfilter\fR <val></span></span>
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2283
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<pre style="margin: 0;">+<span id="LC2283" class="line" lang="mosel"><span class="s1" style="color: #d14;">: Filter out association test results with higher p\-values.</span></span>
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2284
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<pre style="margin: 0;">+<span id="LC2284" class="line" lang="mosel"><span class="s1" style="color: #d14;">.HP</span></span>
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2285
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<pre style="margin: 0;">+<span id="LC2285" class="line" lang="mosel"><span class="s1" style="color: #d14;">\fB\-\-aperm\fR <min perms \- 1> [max perms] [alpha] [beta] [init interval] [slope] :</span></span>
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2286
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<pre style="margin: 0;">+<span id="LC2286" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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2287
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<pre style="margin: 0;">+<span id="LC2287" class="line" lang="mosel"><span class="s1" style="color: #d14;">Set up to six parameters controlling adaptive permutation tests.</span></span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The first two control the minimum and maximum number of permutations that</span></span>
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2289
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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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2290
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<pre style="margin: 0;">+<span id="LC2290" class="line" lang="mosel"><span class="s1" style="color: #d14;">may be run for each variant; default values are 5 and 1000000.</span></span>
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2291
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<pre style="margin: 0;">+<span id="LC2291" class="line" lang="mosel"><span class="s1" style="color: #d14;">.TP</span></span>
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2292
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="mosel"><span class="s1" style="color: #d14;">* The next two control the early termination condition.</span></span>
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<pre style="margin: 0;">+<span id="LC2293" class="line" lang="mosel"><span class="s1" style="color: #d14;">A</span></span>
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2294
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<pre style="margin: 0;">+<span id="LC2294" class="line" lang="mosel"><span class="s1" style="color: #d14;">.IP</span></span>
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2295
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<pre style="margin: 0;">+<span id="LC2295" class="line" lang="mosel"><span class="s1" style="color: #d14;">100% * (1 \- beta/2T) confidence interval is calculated for each empirical</span></span>
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2296
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<pre style="margin: 0;">+<span id="LC2296" class="line" lang="mosel"><span class="s1" style="color: #d14;">p\-value, where T is the total number of variants; whenever this</span></span>
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2297
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<pre style="margin: 0;">+<span id="LC2297" class="line" lang="mosel"><span class="s1" style="color: #d14;">confidence interval doesn'</span><span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">alpha</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">exempted</span> <span class="k" style="font-weight: 600;">from</span></span>
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2298
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<pre style="margin: 0;">+<span id="LC2298" class="line" lang="mosel"><span class="n" style="color: #333;">further</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">testing</span><span class="p">.</span> <span class="n" style="color: #333;">Default</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">are</span> <span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">e</span><span class="p">\-</span><span class="m" style="color: #099;">4.</span></span>
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2299
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<pre style="margin: 0;">+<span id="LC2299" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2300
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<pre style="margin: 0;">+<span id="LC2300" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">last</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">early</span> <span class="n" style="color: #333;">termination</span> <span class="n" style="color: #333;">condition</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">checked</span><span class="p">.</span></span>
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2301
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<pre style="margin: 0;">+<span id="LC2301" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span></span>
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2302
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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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2303
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<pre style="margin: 0;">+<span id="LC2303" class="line" lang="mosel"><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">occurs</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">permutation</span> <span class="p">#</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">next</span> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">occurs</span> <span class="n" style="color: #333;">after</span></span>
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2304
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<pre style="margin: 0;">+<span id="LC2304" class="line" lang="mosel"><span class="p"><</span><span class="n" style="color: #333;">slope</span><span class="p">></span><span class="n" style="color: #333;">p</span> <span class="p">+</span> <span class="p"><</span><span class="n" style="color: #333;">init</span> <span class="n" style="color: #333;">interval</span><span class="p">></span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">permutations</span> <span class="p">(</span><span class="n" style="color: #333;">rounded</span> <span class="n" style="color: #333;">down</span><span class="p">).</span> <span class="n" style="color: #333;">Default</span></span>
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2305
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<pre style="margin: 0;">+<span id="LC2305" class="line" lang="mosel"><span class="n" style="color: #333;">initial</span> <span class="n" style="color: #333;">interval</span> <span class="n" style="color: #333;">is</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">slope</span> <span class="n" style="color: #333;">is</span> <span class="m" style="color: #099;">0.001</span><span class="p">.</span></span>
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2306
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<pre style="margin: 0;">+<span id="LC2306" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2307
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<pre style="margin: 0;">+<span id="LC2307" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mperm</span><span class="p">\-</span><span class="n" style="color: #333;">save</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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2308
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<pre style="margin: 0;">+<span id="LC2308" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Save</span> <span class="n" style="color: #333;">best</span> <span class="k" style="font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">)</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">statistics</span><span class="p">.</span></span>
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2309
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<pre style="margin: 0;">+<span id="LC2309" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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2310
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<pre style="margin: 0;">+<span id="LC2310" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">mperm</span><span class="p">\-</span><span class="n" style="color: #333;">save</span><span class="p">\-</span><span class="n" style="color: #333;">all</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">:</span> <span class="n" style="color: #333;">Save</span> <span class="n" style="color: #333;">all</span> <span class="k" style="font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">)</span> <span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">statistics</span><span class="p">.</span></span>
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2311
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<pre style="margin: 0;">+<span id="LC2311" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<pre style="margin: 0;">+<span id="LC2312" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">p</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">val</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2313
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<pre style="margin: 0;">+<span id="LC2313" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Adjust</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">significant</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">ceiling</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2314
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<pre style="margin: 0;">+<span id="LC2314" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.05</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2315
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<pre style="margin: 0;">+<span id="LC2315" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2316
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<pre style="margin: 0;">+<span id="LC2316" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">r2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p">[</span><span class="n" style="color: #333;">v</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'write'</span><span class="p">]</span> <span class="p">:</span> <span class="n" style="color: #333;">Adjust</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">significant</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">r</span><span class="p">^</span><span class="m" style="color: #099;">2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2317
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<pre style="margin: 0;">+<span id="LC2317" class="line" lang="mosel"><span class="n" style="color: #333;">ceiling</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.5</span><span class="p">).</span> <span class="s1" style="color: #d14;">'write'</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">violating</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2318
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<pre style="margin: 0;">+<span id="LC2318" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2319
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<pre style="margin: 0;">+<span id="LC2319" class="line" lang="mosel"><span class="n" style="color: #333;">pairs</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">dumped</span> <span class="k" style="font-weight: 600;">to</span> <span class="p"><</span><span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">prefix</span><span class="p">>.</span><span class="n" style="color: #333;">ldset</span><span class="p">.</span></span>
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2320
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<pre style="margin: 0;">+<span id="LC2320" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2321
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<pre style="margin: 0;">+<span id="LC2321" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="k" style="font-weight: 600;">max</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">ct</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2322
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<pre style="margin: 0;">+<span id="LC2322" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Adjust</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">maximum</span> <span class="p">#</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">significant</span> <span class="n" style="color: #333;">variants</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2323
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<pre style="margin: 0;">+<span id="LC2323" class="line" lang="mosel"><span class="n" style="color: #333;">considered</span> <span class="n" style="color: #333;">per</span> <span class="k" style="font-weight: 600;">set</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">5</span><span class="p">).</span></span>
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2324
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<pre style="margin: 0;">+<span id="LC2324" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2325
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<pre style="margin: 0;">+<span id="LC2325" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="k" style="font-weight: 600;">set</span><span class="p">\-</span><span class="n" style="color: #333;">test</span><span class="p">\-</span><span class="n" style="color: #333;">lambda</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">v</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2326
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<pre style="margin: 0;">+<span id="LC2326" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">genomic</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">correction</span> <span class="n" style="color: #333;">for</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">test</span><span class="p">.</span></span>
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2327
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<pre style="margin: 0;">+<span id="LC2327" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2328
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<pre style="margin: 0;">+<span id="LC2328" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">border</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">kbs</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2329
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<pre style="margin: 0;">+<span id="LC2329" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Extend</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">annotate</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">intervals</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">given</span> <span class="p">#</span> <span class="n" style="color: #333;">kbs</span><span class="p">.</span></span>
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2330
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<pre style="margin: 0;">+<span id="LC2330" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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2331
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<pre style="margin: 0;">+<span id="LC2331" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">annotate</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">nm</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">annotate</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ID</span> <span class="n" style="color: #333;">field</span> <span class="n" style="color: #333;">name</span><span class="p">.</span></span>
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2332
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<pre style="margin: 0;">+<span id="LC2332" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2333
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<pre style="margin: 0;">+<span id="LC2333" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">p1</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">pval</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">index</span> <span class="n" style="color: #333;">var</span><span class="p">.</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">ceiling</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">e</span><span class="p">\-</span><span class="m" style="color: #099;">4</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2334
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<pre style="margin: 0;">+<span id="LC2334" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2335
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<pre style="margin: 0;">+<span id="LC2335" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">p2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">pval</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">secondary</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">threshold</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.01</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2336
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<pre style="margin: 0;">+<span id="LC2336" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2337
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<pre style="margin: 0;">+<span id="LC2337" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">r2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">r</span><span class="p">^</span><span class="m" style="color: #099;">2</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2338
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<pre style="margin: 0;">+<span id="LC2338" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">r</span><span class="p">^</span><span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">threshold</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">0.5</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2339
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<pre style="margin: 0;">+<span id="LC2339" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2340
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<pre style="margin: 0;">+<span id="LC2340" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">kb</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">kbs</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2341
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<pre style="margin: 0;">+<span id="LC2341" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">kb</span> <span class="n" style="color: #333;">radius</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">250</span><span class="p">).</span></span>
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2342
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<pre style="margin: 0;">+<span id="LC2342" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2343
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<pre style="margin: 0;">+<span id="LC2343" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2344
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<pre style="margin: 0;">+<span id="LC2344" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ID</span> <span class="n" style="color: #333;">field</span> <span class="n" style="color: #333;">name</span> <span class="p">(</span><span class="n" style="color: #333;">default</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2345
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<pre style="margin: 0;">+<span id="LC2345" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'SNP'</span><span class="p">).</span> <span class="k" style="font-weight: 600;">With</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">field</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">earlier</span> <span class="n" style="color: #333;">names</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2346
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<pre style="margin: 0;">+<span id="LC2346" class="line" lang="mosel"><span class="n" style="color: #333;">take</span> <span class="n" style="color: #333;">precedence</span> <span class="n" style="color: #333;">over</span> <span class="n" style="color: #333;">later</span> <span class="n" style="color: #333;">ones</span><span class="p">.</span></span>
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2347
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<pre style="margin: 0;">+<span id="LC2347" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2348
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<pre style="margin: 0;">+<span id="LC2348" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">name</span><span class="p">...></span></span>
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2349
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<pre style="margin: 0;">+<span id="LC2349" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">field</span> <span class="n" style="color: #333;">name</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="s1" style="color: #d14;">'P'</span><span class="p">).</span></span>
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2350
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<pre style="margin: 0;">+<span id="LC2350" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2351
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<pre style="margin: 0;">+<span id="LC2351" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">allow</span><span class="p">\-</span><span class="n" style="color: #333;">overlap</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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2352
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<pre style="margin: 0;">+<span id="LC2352" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Let</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">non</span><span class="p">\-</span><span class="n" style="color: #333;">index</span> <span class="n" style="color: #333;">vars</span><span class="p">.</span> <span class="n" style="color: #333;">join</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">clumps</span><span class="p">.</span></span>
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2353
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<pre style="margin: 0;">+<span id="LC2353" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2354
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<pre style="margin: 0;">+<span id="LC2354" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">verbose</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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2355
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<pre style="margin: 0;">+<span id="LC2355" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Request</span> <span class="n" style="color: #333;">extended</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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2356
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<pre style="margin: 0;">+<span id="LC2356" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2357
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<pre style="margin: 0;">+<span id="LC2357" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">annotate</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">hdr</span><span class="p">...></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Include</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">extra</span> <span class="n" style="color: #333;">fields</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">verbose</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2358
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<pre style="margin: 0;">+<span id="LC2358" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">best</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">reports</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Field</span> <span class="n" style="color: #333;">names</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2359
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<pre style="margin: 0;">+<span id="LC2359" class="line" lang="mosel"><span class="n" style="color: #333;">separated</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">spaces</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">commas</span><span class="p">.)</span></span>
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2360
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<pre style="margin: 0;">+<span id="LC2360" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2361
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<pre style="margin: 0;">+<span id="LC2361" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="k" style="font-weight: 600;">range</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2362
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<pre style="margin: 0;">+<span id="LC2362" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Report</span> <span class="n" style="color: #333;">overlaps</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">clumps</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">regions</span><span class="p">.</span></span>
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2363
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<pre style="margin: 0;">+<span id="LC2363" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2364
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<pre style="margin: 0;">+<span id="LC2364" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="k" style="font-weight: 600;">range</span><span class="p">\-</span><span class="n" style="color: #333;">border</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">kb</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Stretch</span> <span class="n" style="color: #333;">regions</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="k" style="font-weight: 600;">range</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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2365
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<pre style="margin: 0;">+<span id="LC2365" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2366
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<pre style="margin: 0;">+<span id="LC2366" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">index</span><span class="p">\-</span><span class="n" style="color: #333;">first</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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2367
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<pre style="margin: 0;">+<span id="LC2367" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Extract</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">index</span> <span class="n" style="color: #333;">vars</span><span class="p">.</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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2368
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<pre style="margin: 0;">+<span id="LC2368" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2369
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<pre style="margin: 0;">+<span id="LC2369" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">replicate</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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2370
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<pre style="margin: 0;">+<span id="LC2370" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Exclude</span> <span class="n" style="color: #333;">clumps</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">secondary</span> <span class="n" style="color: #333;">results</span></span>
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2371
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<pre style="margin: 0;">+<span id="LC2371" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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2372
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<pre style="margin: 0;">+<span id="LC2372" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2373
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<pre style="margin: 0;">+<span id="LC2373" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\-</span><span class="n" style="color: #333;">best</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2374
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<pre style="margin: 0;">+<span id="LC2374" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Report</span> <span class="n" style="color: #333;">best</span> <span class="n" style="color: #333;">proxy</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">each</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">clump</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">index</span> <span class="n" style="color: #333;">var</span><span class="p">.</span></span>
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2375
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<pre style="margin: 0;">+<span id="LC2375" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2376
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<pre style="margin: 0;">+<span id="LC2376" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">chr</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">chromosome</span><span class="p">,</span> <span class="n" style="color: #333;">variant</span></span>
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2377
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<pre style="margin: 0;">+<span id="LC2377" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2378
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<pre style="margin: 0;">+<span id="LC2378" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2379
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<pre style="margin: 0;">+<span id="LC2379" class="line" lang="mosel"><span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">A1</span><span class="p">/</span><span class="n" style="color: #333;">A2</span> <span class="n" style="color: #333;">allele</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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2380
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<pre style="margin: 0;">+<span id="LC2380" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2381
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<pre style="margin: 0;">+<span id="LC2381" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">bp</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span></span>
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2382
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<pre style="margin: 0;">+<span id="LC2382" class="line" lang="mosel"><span class="n" style="color: #333;">standard</span> <span class="n" style="color: #333;">error</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span><span class="p">/</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">effective</span> <span class="n" style="color: #333;">sample</span></span>
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2383
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<pre style="margin: 0;">+<span id="LC2383" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2384
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<pre style="margin: 0;">+<span id="LC2384" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">a1</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span></span>
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2385
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<pre style="margin: 0;">+<span id="LC2385" class="line" lang="mosel"><span class="n" style="color: #333;">size</span> <span class="n" style="color: #333;">field</span> <span class="n" style="color: #333;">names</span><span class="p">.</span></span>
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2386
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<pre style="margin: 0;">+<span id="LC2386" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2387
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<pre style="margin: 0;">+<span id="LC2387" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">a2</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span></span>
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2388
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<pre style="margin: 0;">+<span id="LC2388" class="line" lang="mosel"><span class="n" style="color: #333;">Defaults</span> <span class="n" style="color: #333;">are</span> <span class="s1" style="color: #d14;">'CHR'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'SNP'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'BP'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'A1'</span><span class="p">,</span></span>
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2389
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2390
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<pre style="margin: 0;">+<span id="LC2390" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2391
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<pre style="margin: 0;">+<span id="LC2391" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'A2'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'P'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'SE'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'NMISS'</span><span class="p">,</span></span>
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2392
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<pre style="margin: 0;">+<span id="LC2392" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2393
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<pre style="margin: 0;">+<span id="LC2393" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">se</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span></span>
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2394
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<pre style="margin: 0;">+<span id="LC2394" class="line" lang="mosel"><span class="n" style="color: #333;">respectively</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">multiple</span> <span class="k" style="font-weight: 600;">parameters</span></span>
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2395
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<pre style="margin: 0;">+<span id="LC2395" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2396
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<pre style="margin: 0;">+<span id="LC2396" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">ess</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">...></span></span>
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2397
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<pre style="margin: 0;">+<span id="LC2397" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">given</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">flags</span><span class="p">,</span> <span class="n" style="color: #333;">earlier</span> <span class="n" style="color: #333;">names</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2398
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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="mosel"><span class="n" style="color: #333;">take</span> <span class="n" style="color: #333;">precedence</span> <span class="n" style="color: #333;">over</span> <span class="n" style="color: #333;">later</span> <span class="n" style="color: #333;">ones</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2399
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<pre style="margin: 0;">+<span id="LC2399" class="line" lang="mosel"><span class="n" style="color: #333;">Note</span> <span class="n" style="color: #333;">that</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">numbers</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">cases</span> <span class="k" style="font-weight: 600;">and</span></span>
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2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="mosel"><span class="n" style="color: #333;">controls</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">unequal</span><span class="p">,</span> <span class="n" style="color: #333;">effective</span> <span class="n" style="color: #333;">sample</span></span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="mosel"><span class="n" style="color: #333;">size</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span></span>
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2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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2403
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<pre style="margin: 0;">+<span id="LC2403" class="line" lang="mosel"><span class="m" style="color: #099;">4</span> <span class="p">/</span> <span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">/<#</span> <span class="n" style="color: #333;">cases</span><span class="p">></span> <span class="p">+</span> <span class="m" style="color: #099;">1</span><span class="p">/<#</span> <span class="n" style="color: #333;">controls</span><span class="p">>).</span></span>
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2404
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<pre style="margin: 0;">+<span id="LC2404" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2405
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<pre style="margin: 0;">+<span id="LC2405" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">meta</span><span class="p">\-</span><span class="n" style="color: #333;">analysis</span><span class="p">\-</span><span class="n" style="color: #333;">report</span><span class="p">\-</span><span class="n" style="color: #333;">dups</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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2406
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<pre style="margin: 0;">+<span id="LC2406" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">appears</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">times</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">that</span><span class="p">.</span></span>
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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="k" style="font-weight: 600;">list</span><span class="p">\-</span><span class="n" style="color: #333;">border</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">kbs</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Extend</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="n" style="color: #333;">report</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">regions</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">given</span> <span class="p">#</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">kbs</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2411
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<pre style="margin: 0;">+<span id="LC2411" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="n" style="color: #333;">subset</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">filename</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">gene</span> <span class="n" style="color: #333;">name</span> <span class="n" style="color: #333;">subset</span> <span class="n" style="color: #333;">for</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="n" style="color: #333;">report</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2414
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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2415
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<pre style="margin: 0;">+<span id="LC2415" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="n" style="color: #333;">report</span><span class="p">\-</span><span class="n" style="color: #333;">snp</span><span class="p">\-</span><span class="n" style="color: #333;">field</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gene</span><span class="p">\-</span><span class="n" style="color: #333;">report</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ID</span> <span class="n" style="color: #333;">field</span> <span class="n" style="color: #333;">name</span> <span class="p">(</span><span class="n" style="color: #333;">default</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2416
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<pre style="margin: 0;">+<span id="LC2416" class="line" lang="mosel"><span class="p">\&</span><span class="s1" style="color: #d14;">'SNP'</span><span class="p">).</span> <span class="n" style="color: #333;">Only</span> <span class="n" style="color: #333;">relevant</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">extract</span><span class="p">\</span><span class="n" style="color: #333;">fR</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2417
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<pre style="margin: 0;">+<span id="LC2417" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2418
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<pre style="margin: 0;">+<span id="LC2418" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">gap</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">kbs</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2419
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<pre style="margin: 0;">+<span id="LC2419" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="s2" style="color: #d14;">"\-\-fast\-epistasis case\-only"</span> <span class="k" style="font-weight: 600;">min</span><span class="p">.</span> <span class="n" style="color: #333;">gap</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">1000</span><span class="p">).</span></span>
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2420
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<pre style="margin: 0;">+<span id="LC2420" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2421
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<pre style="margin: 0;">+<span id="LC2421" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">epi1</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-[</span><span class="n" style="color: #333;">fast</span><span class="p">\-]</span><span class="n" style="color: #333;">epistasis</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="n" style="color: #333;">reporting</span> <span class="n" style="color: #333;">threshold</span> <span class="p">(</span><span class="n" style="color: #333;">default</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2422
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<pre style="margin: 0;">+<span id="LC2422" class="line" lang="mosel"><span class="m" style="color: #099;">5</span><span class="n" style="color: #333;">e</span><span class="p">\-</span><span class="m" style="color: #099;">6</span> <span class="n" style="color: #333;">for</span> <span class="s1" style="color: #d14;">'boost'</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">e</span><span class="p">\-</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">otherwise</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2423
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<pre style="margin: 0;">+<span id="LC2423" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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2424
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<pre style="margin: 0;">+<span id="LC2424" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">epi2</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">threshold</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">contributing</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">SIG_E</span> <span class="k" style="font-weight: 600;">count</span> <span class="p">(</span><span class="n" style="color: #333;">def</span><span class="p">.</span> <span class="m" style="color: #099;">0.01</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2425
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<pre style="margin: 0;">+<span id="LC2425" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2426
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<pre style="margin: 0;">+<span id="LC2426" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">je</span><span class="p">\-</span><span class="n" style="color: #333;">cellmin</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">required</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">observations</span> <span class="n" style="color: #333;">per</span> <span class="m" style="color: #099;">3</span><span class="n" style="color: #333;">x3x2</span> <span class="n" style="color: #333;">contingency</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2427
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<pre style="margin: 0;">+<span id="LC2427" class="line" lang="mosel"><span class="n" style="color: #333;">table</span> <span class="n" style="color: #333;">cell</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">joint</span><span class="p">\-</span><span class="n" style="color: #333;">effects</span> <span class="n" style="color: #333;">test</span> <span class="p">(</span><span class="n" style="color: #333;">default</span> <span class="m" style="color: #099;">5</span><span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2428
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<pre style="margin: 0;">+<span id="LC2428" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2429
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<pre style="margin: 0;">+<span id="LC2429" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">q</span><span class="p">\-</span><span class="n" style="color: #333;">score</span><span class="p">\-</span><span class="k" style="font-weight: 600;">range</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">file</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">file</span><span class="p">></span> <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">[</span><span class="s1" style="color: #d14;">'header'</span><span class="p">]</span> <span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2430
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<pre style="margin: 0;">+<span id="LC2430" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2431
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<pre style="margin: 0;">+<span id="LC2431" class="line" lang="mosel"><span class="n" style="color: #333;">Apply</span> <span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">score</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">subset</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">variants</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">primary</span> <span class="n" style="color: #333;">score</span> <span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">based</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2432
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<pre style="margin: 0;">+<span id="LC2432" class="line" lang="mosel"><span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">ranges</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2433
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<pre style="margin: 0;">+<span id="LC2433" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">labels</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">column</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span></span>
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2434
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<pre style="margin: 0;">+<span id="LC2434" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2435
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<pre style="margin: 0;">+<span id="LC2435" class="line" lang="mosel"><span class="n" style="color: #333;">lower</span> <span class="n" style="color: #333;">bounds</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">second</span> <span class="n" style="color: #333;">column</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">upper</span> <span class="n" style="color: #333;">bounds</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">third</span> <span class="n" style="color: #333;">column</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2436
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<pre style="margin: 0;">+<span id="LC2436" class="line" lang="mosel"><span class="n" style="color: #333;">Lines</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">too</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">entries</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">nonnumeric</span> <span class="n" style="color: #333;">values</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">second</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">third</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2437
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<pre style="margin: 0;">+<span id="LC2437" class="line" lang="mosel"><span class="n" style="color: #333;">column</span><span class="p">,</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">ignored</span><span class="p">.</span></span>
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2438
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<pre style="margin: 0;">+<span id="LC2438" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2439
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<pre style="margin: 0;">+<span id="LC2439" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">second</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variant</span> <span class="n" style="color: #333;">ID</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">each</span></span>
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2440
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<pre style="margin: 0;">+<span id="LC2440" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<pre style="margin: 0;">+<span id="LC2441" class="line" lang="mosel"><span class="n" style="color: #333;">nonempty</span> <span class="n" style="color: #333;">line</span> <span class="p">(</span><span class="n" style="color: #333;">except</span> <span class="n" style="color: #333;">possibly</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span><span class="p">).</span></span>
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<pre style="margin: 0;">+<span id="LC2442" class="line" lang="mosel"><span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">IDs</span> <span class="n" style="color: #333;">are</span> <span class="nb" style="color: #0086b3;">read</span> <span class="k" style="font-weight: 600;">from</span></span>
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2443
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<pre style="margin: 0;">+<span id="LC2443" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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2444
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<pre style="margin: 0;">+<span id="LC2444" class="line" lang="mosel"><span class="n" style="color: #333;">column</span> <span class="p">#</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">are</span> <span class="nb" style="color: #0086b3;">read</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">column</span> <span class="p">#</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">i</span> <span class="n" style="color: #333;">defaults</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2445
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<pre style="margin: 0;">+<span id="LC2445" class="line" lang="mosel"><span class="n" style="color: #333;">j</span> <span class="n" style="color: #333;">defaults</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">i</span><span class="p">+</span><span class="m" style="color: #099;">1.</span> <span class="n" style="color: #333;">The</span> <span class="s1" style="color: #d14;">'header'</span> <span class="n" style="color: #333;">modifier</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">nonempty</span> <span class="n" style="color: #333;">line</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2446
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<pre style="margin: 0;">+<span id="LC2446" class="line" lang="mosel"><span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">skipped</span><span class="p">.</span></span>
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2447
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<pre style="margin: 0;">+<span id="LC2447" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2448
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<pre style="margin: 0;">+<span id="LC2448" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">R</span><span class="p">\-</span><span class="n" style="color: #333;">port</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">port</span> <span class="p">#></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2449
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<pre style="margin: 0;">+<span id="LC2449" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Connect</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Rserve</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">port</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">6311.</span></span>
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2450
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<pre style="margin: 0;">+<span id="LC2450" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2451
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<pre style="margin: 0;">+<span id="LC2451" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">R</span><span class="p">\-</span><span class="n" style="color: #333;">host</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">host</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2452
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<pre style="margin: 0;">+<span id="LC2452" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Connect</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Rserve</span> <span class="n" style="color: #333;">host</span><span class="p">.</span></span>
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2453
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<pre style="margin: 0;">+<span id="LC2453" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2454
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<pre style="margin: 0;">+<span id="LC2454" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">R</span><span class="p">\-</span><span class="n" style="color: #333;">socket</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">sock</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2455
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<pre style="margin: 0;">+<span id="LC2455" class="line" lang="mosel"><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">Connect</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Rserve</span> <span class="n" style="color: #333;">socket</span><span class="p">.</span></span>
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2456
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<pre style="margin: 0;">+<span id="LC2456" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2457
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<pre style="margin: 0;">+<span id="LC2457" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">parallel</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">k</span><span class="p">></span> <span class="p"><</span><span class="n" style="color: #333;">n</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Divide</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">matrix</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">n</span> <span class="n" style="color: #333;">pieces</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">compute</span></span>
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2458
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<pre style="margin: 0;">+<span id="LC2458" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">kth</span> <span class="n" style="color: #333;">piece</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">primary</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">+<span id="LC2459" class="line" lang="mosel"><span class="n" style="color: #333;">piece</span> <span class="n" style="color: #333;">number</span> <span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="n" style="color: #333;">plink</span><span class="p">.</span><span class="n" style="color: #333;">rel</span><span class="m" style="color: #099;">.13</span> <span class="k" style="font-weight: 600;">or</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2460
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<pre style="margin: 0;">+<span id="LC2460" class="line" lang="mosel"><span class="n" style="color: #333;">plink</span><span class="p">.</span><span class="n" style="color: #333;">rel</span><span class="m" style="color: #099;">.13</span><span class="p">.</span><span class="n" style="color: #333;">gz</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">k</span> <span class="n" style="color: #333;">is</span> <span class="m" style="color: #099;">13.</span> <span class="n" style="color: #333;">Concatenating</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">files</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2461
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<pre style="margin: 0;">+<span id="LC2461" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">yield</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">full</span> <span class="n" style="color: #333;">matrix</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">interest</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Yes</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2462
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<pre style="margin: 0;">+<span id="LC2462" class="line" lang="mosel"><span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">done</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">unzipping</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2463
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<pre style="margin: 0;">+<span id="LC2463" class="line" lang="mosel"><span class="n" style="color: #333;">N</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">generally</span> <span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">directly</span> <span class="nb" style="color: #0086b3;">write</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2464
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<pre style="margin: 0;">+<span id="LC2464" class="line" lang="mosel"><span class="n" style="color: #333;">symmetric</span> <span class="n" style="color: #333;">square</span> <span class="n" style="color: #333;">matrix</span><span class="p">.</span> <span class="n" style="color: #333;">Choose</span> <span class="n" style="color: #333;">square0</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">triangle</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2465
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<pre style="margin: 0;">+<span id="LC2465" class="line" lang="mosel"><span class="n" style="color: #333;">shape</span> <span class="n" style="color: #333;">instead</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">postprocess</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">necessary</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2466
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<pre style="margin: 0;">+<span id="LC2466" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2467
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<pre style="margin: 0;">+<span id="LC2467" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">memory</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2468
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<pre style="margin: 0;">+<span id="LC2468" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">MB</span><span class="p">,</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">initial</span> <span class="n" style="color: #333;">workspace</span> <span class="n" style="color: #333;">malloc</span> <span class="n" style="color: #333;">attempt</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2469
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<pre style="margin: 0;">+<span id="LC2469" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">Practically</span> <span class="n" style="color: #333;">mandatory</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">GNU</span> <span class="n" style="color: #333;">parallel</span><span class="p">.)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2470
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<pre style="margin: 0;">+<span id="LC2470" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2471
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<pre style="margin: 0;">+<span id="LC2471" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">threads</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2472
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<pre style="margin: 0;">+<span id="LC2472" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">concurrent</span> <span class="n" style="color: #333;">threads</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2473
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<pre style="margin: 0;">+<span id="LC2473" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">known</span> <span class="n" style="color: #333;">limitation</span><span class="p">:</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">BLAS</span><span class="p">/</span><span class="n" style="color: #333;">LAPACK</span> <span class="n" style="color: #333;">linear</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2474
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<pre style="margin: 0;">+<span id="LC2474" class="line" lang="mosel"><span class="n" style="color: #333;">algebra</span> <span class="n" style="color: #333;">operations</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">multithreaded</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">way</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">PLINK</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2475
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<pre style="margin: 0;">+<span id="LC2475" class="line" lang="mosel"><span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">control</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">problematic</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">should</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2476
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<pre style="margin: 0;">+<span id="LC2476" class="line" lang="mosel"><span class="n" style="color: #333;">recompile</span> <span class="n" style="color: #333;">against</span> <span class="n" style="color: #333;">single</span><span class="p">\-</span><span class="n" style="color: #333;">threaded</span> <span class="n" style="color: #333;">BLAS</span><span class="p">/</span><span class="n" style="color: #333;">LAPACK</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2477
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<pre style="margin: 0;">+<span id="LC2477" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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2478
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<pre style="margin: 0;">+<span id="LC2478" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">d</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">char</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2479
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<pre style="margin: 0;">+<span id="LC2479" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Change</span> <span class="n" style="color: #333;">variant</span><span class="p">/</span><span class="n" style="color: #333;">covariate</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">delimiter</span> <span class="p">(</span><span class="n" style="color: #333;">normally</span> <span class="s1" style="color: #d14;">'\-'</span><span class="p">).</span></span>
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2480
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<pre style="margin: 0;">+<span id="LC2480" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2481
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<pre style="margin: 0;">+<span id="LC2481" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">seed</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">...></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2482
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<pre style="margin: 0;">+<span id="LC2482" class="line" lang="mosel"><span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="nb" style="color: #0086b3;">random</span> <span class="n" style="color: #333;">number</span> <span class="n" style="color: #333;">seed</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">).</span> <span class="n" style="color: #333;">Each</span> <span class="n" style="color: #333;">value</span> <span class="n" style="color: #333;">must</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">an</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2483
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<pre style="margin: 0;">+<span id="LC2483" class="line" lang="mosel"><span class="k" style="font-weight: 600;">integer</span> <span class="n" style="color: #333;">between</span> <span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4294967295</span> <span class="n" style="color: #333;">inclusive</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2484
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<pre style="margin: 0;">+<span id="LC2484" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2485
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<pre style="margin: 0;">+<span id="LC2485" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">perm</span><span class="p">\-</span><span class="n" style="color: #333;">batch</span><span class="p">\-</span><span class="n" style="color: #333;">size</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">val</span><span class="p">></span> <span class="p">:</span> <span class="k" style="font-weight: 600;">Set</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">permutations</span> <span class="n" style="color: #333;">per</span> <span class="n" style="color: #333;">batch</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">some</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2486
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<pre style="margin: 0;">+<span id="LC2486" class="line" lang="mosel"><span class="n" style="color: #333;">permutation</span> <span class="n" style="color: #333;">tests</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2487
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<pre style="margin: 0;">+<span id="LC2487" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">HP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2488
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<pre style="margin: 0;">+<span id="LC2488" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">output</span><span class="p">\-</span><span class="k" style="font-weight: 600;">min</span><span class="p">\-</span><span class="n" style="color: #333;">p</span><span class="p">\</span><span class="n" style="color: #333;">fR</span> <span class="p"><</span><span class="n" style="color: #333;">p</span><span class="p">></span> <span class="p">:</span> <span class="n" style="color: #333;">Specify</span> <span class="n" style="color: #333;">minimum</span> <span class="n" style="color: #333;">p</span><span class="p">\-</span><span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">to</span> <span class="nb" style="color: #0086b3;">write</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">reports</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2489
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<pre style="margin: 0;">+<span id="LC2489" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2490
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<pre style="margin: 0;">+<span id="LC2490" class="line" lang="mosel"><span class="p">\</span><span class="n" style="color: #333;">fB</span><span class="p">\-\-</span><span class="n" style="color: #333;">debug</span><span class="p">\</span><span class="n" style="color: #333;">fR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2491
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<pre style="margin: 0;">+<span id="LC2491" class="line" lang="mosel"><span class="p">:</span> <span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">slower</span><span class="p">,</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">crash</span><span class="p">\-</span><span class="n" style="color: #333;">resistant</span> <span class="n" style="color: #333;">logging</span> <span class="n" style="color: #333;">method</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2492
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<pre style="margin: 0;">+<span id="LC2492" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">PP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2493
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<pre style="margin: 0;">+<span id="LC2493" class="line" lang="mosel"><span class="n" style="color: #333;">Primary</span> <span class="n" style="color: #333;">methods</span> <span class="n" style="color: #333;">paper</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2494
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<pre style="margin: 0;">+<span id="LC2494" class="line" lang="mosel"><span class="n" style="color: #333;">Chang</span> <span class="n" style="color: #333;">CC</span><span class="p">,</span> <span class="n" style="color: #333;">Chow</span> <span class="n" style="color: #333;">CC</span><span class="p">,</span> <span class="n" style="color: #333;">Tellier</span> <span class="n" style="color: #333;">LCAM</span><span class="p">,</span> <span class="n" style="color: #333;">Vattikuti</span> <span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="n" style="color: #333;">Purcell</span> <span class="n" style="color: #333;">SM</span><span class="p">,</span> <span class="n" style="color: #333;">Lee</span> <span class="n" style="color: #333;">JJ</span> <span class="p">(</span><span class="m" style="color: #099;">2015</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2495
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<pre style="margin: 0;">+<span id="LC2495" class="line" lang="mosel"><span class="n" style="color: #333;">Second</span><span class="p">\-</span><span class="n" style="color: #333;">generation</span> <span class="n" style="color: #333;">PLINK</span><span class="p">:</span> <span class="n" style="color: #333;">rising</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">challenge</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">larger</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">richer</span> <span class="n" style="color: #333;">datasets</span><span class="p">.</span></span>
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2496
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<pre style="margin: 0;">+<span id="LC2496" class="line" lang="mosel"><span class="n" style="color: #333;">GigaScience</span><span class="p">,</span> <span class="m" style="color: #099;">4.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2497
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<pre style="margin: 0;">+<span id="LC2497" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">PP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2498
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<pre style="margin: 0;">+<span id="LC2498" class="line" lang="mosel"><span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">further</span> <span class="n" style="color: #333;">documentation</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">support</span><span class="p">,</span> <span class="n" style="color: #333;">consult</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">main</span> <span class="n" style="color: #333;">webpage</span></span>
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2499
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<pre style="margin: 0;">+<span id="LC2499" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">cog</span><span class="p">\-</span><span class="n" style="color: #333;">genomics</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">plink</span><span class="p">/</span><span class="m" style="color: #099;">1.9</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">and</span><span class="p">/</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">mailing</span> <span class="k" style="font-weight: 600;">list</span></span>
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2500
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<pre style="margin: 0;">+<span id="LC2500" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">google</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">d</span><span class="p">/</span><span class="n" style="color: #333;">forum</span><span class="p">/</span><span class="n" style="color: #333;">plink2</span><span class="p">\-</span><span class="n" style="color: #333;">users</span> <span class="p">).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2501
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<pre style="margin: 0;">+<span id="LC2501" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">SH</span> <span class="s2" style="color: #d14;">"SEE ALSO"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2502
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<pre style="margin: 0;">+<span id="LC2502" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">full</span> <span class="n" style="color: #333;">documentation</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2503
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<pre style="margin: 0;">+<span id="LC2503" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">B</span> <span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">v1</span><span class="m" style="color: #099;">.90</span><span class="n" style="color: #333;">b6</span><span class="m" style="color: #099;">.16</span> <span class="m" style="color: #099;">64</span><span class="p">-</span><span class="n" style="color: #333;">bit</span> <span class="p">(</span><span class="m" style="color: #099;">19</span> <span class="n" style="color: #333;">Feb</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2504
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<pre style="margin: 0;">+<span id="LC2504" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">maintained</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Texinfo</span> <span class="n" style="color: #333;">manual</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2505
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<pre style="margin: 0;">+<span id="LC2505" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">B</span> <span class="n" style="color: #333;">info</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2506
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<pre style="margin: 0;">+<span id="LC2506" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2507
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<pre style="margin: 0;">+<span id="LC2507" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">B</span> <span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">v1</span><span class="m" style="color: #099;">.90</span><span class="n" style="color: #333;">b6</span><span class="m" style="color: #099;">.16</span> <span class="m" style="color: #099;">64</span><span class="p">-</span><span class="n" style="color: #333;">bit</span> <span class="p">(</span><span class="m" style="color: #099;">19</span> <span class="n" style="color: #333;">Feb</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2508
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<pre style="margin: 0;">+<span id="LC2508" class="line" lang="mosel"><span class="n" style="color: #333;">programs</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">properly</span> <span class="n" style="color: #333;">installed</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">site</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="nf" style="color: #900; font-weight: 600;">command</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2509
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<pre style="margin: 0;">+<span id="LC2509" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">IP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2510
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<pre style="margin: 0;">+<span id="LC2510" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">B</span> <span class="n" style="color: #333;">info</span> <span class="n" style="color: #333;">PLINK</span> <span class="n" style="color: #333;">v1</span><span class="m" style="color: #099;">.90</span><span class="n" style="color: #333;">b6</span><span class="m" style="color: #099;">.16</span> <span class="m" style="color: #099;">64</span><span class="p">-</span><span class="n" style="color: #333;">bit</span> <span class="p">(</span><span class="m" style="color: #099;">19</span> <span class="n" style="color: #333;">Feb</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2511
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<pre style="margin: 0;">+<span id="LC2511" class="line" lang="mosel"><span class="p">.</span><span class="n" style="color: #333;">PP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2512
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<pre style="margin: 0;">+<span id="LC2512" class="line" lang="mosel"><span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">give</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">access</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">complete</span> <span class="n" style="color: #333;">manual</span><span class="p">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/plink1-9/-/commit/391c3a96b4532fd9432ae9693b685d0113cda012#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,12 +17,16 @@ override_dh_auto_clean:</td>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_auto_build:</span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh_auto_build</span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> mv plink plink1.9</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> help2man --no-discard-stderr --name="whole genome SNP analysis" ./plink1.9 > plink1.9.1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"># help2man 1.47.13 is not able anymore do generate a clean manpage for plink1.9</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"># which lead to several lintian warnings and more annoying the auto-generated</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># manpage is installed by debhelper in the wrong section due to</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># https://bugs.debian.org/958343</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"># help2man --no-discard-stderr --name="whole genome SNP analysis" ./plink1.9 > plink1.9.1</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> dh_installman plink1.9.1</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> dh_installman <span class="idiff left right">debian/</span>plink1.9.1</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> dh_installchangelogs debian/upstream.docs/upstream.changelog</span></pre>
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