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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/c0beb5609eb43b85877f3288c149c83d5ba85bd7">c0beb560</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-04-21T11:25:02+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not generate manpage for plink2 with help2man
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<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/01274352f062d9c7b637cba5d737dcefc3d23012">01274352</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2020-04-21T11:29:58+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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debian/plink2.1
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/7f9b980e5aefd8fa948ab9571a95ce7ebc1c4bc5...01274352f062d9c7b637cba5d737dcefc3d23012#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">plink2 (2.00~a3-200409+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plink2 (2.00~a3-200409+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> <span class="idiff left right">Fri, 27 Mar 2020 08:44:27 +01</span>00</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> <span class="idiff left right">Tue, 21 Apr 2020 11:29:42 +02</span>00</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">plink2 (2.00~a3-200217+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<li id="b0602b1ce4098d4f68de706a31d115f4d3f9bba3">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/7f9b980e5aefd8fa948ab9571a95ce7ebc1c4bc5...01274352f062d9c7b637cba5d737dcefc3d23012#b0602b1ce4098d4f68de706a31d115f4d3f9bba3"><strong>debian/plink2.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH PLINK "1" "March 2020" "PLINK v2.00a3 64-bit (9 Apr 2020)" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">PLINK \- whole genome SNP analysis</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">PLINK v2.00a3 64\-bit (9 Apr 2020) www.cog\-genomics.org/plink/2.0/</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">(C) 2005\-2020 Shaun Purcell, Christopher Chang GNU General Public License v3</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">In the command line flag definitions that follow,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">* <angle brackets> denote a required parameter, where the text between the</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.IP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">angle brackets describes its nature.</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">* ['square brackets + single\-quotes'] denotes an optional modifier.</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Use the</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.IP</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">EXACT text in the quotes.</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">* [{bar|separated|braced|bracketed|values}] denotes a collection of mutually</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">exclusive optional modifiers (again, the exact text must be used).</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">When</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">there are no outer square brackets, one of the choices must be selected.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.IP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">* ['quoted_text='<description of value>] denotes an optional modifier that</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">must begin with the quoted text, and be followed by a value with no</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">whitespace in between. '|' may also be used here to indicate mutually</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">exclusive options.</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">* [square brackets without quotes or braces] denote an optional parameter,</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.IP</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">where the text between the brackets describes its nature.</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.IP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">* An ellipsis (...) indicates that you may enter multiple arguments of the</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.IP</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">specified type.</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.IP</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">* A "column set descriptor" is either</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.IP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">1. a comma\-separated sequence of column set names; this is interpreted as</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.IP</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">the full list of column sets to include.</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.IP</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">2. a comma\-separated sequence of column set names, all preceded by '+' or</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\&'\-'; this is interpreted as a list of changes to the default.</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...]</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">plink2 \fB\-\-help\fR [flag name(s)...]</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Most PLINK runs require exactly one main input fileset. The following flags</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">are available for defining its form and location:</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-\-pfile\fR <prefix> ['vzs']</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">: Specify .pgen + .pvar[.zst] + .psam prefix.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">\fB\-\-pgen\fR <filename></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">: Specify full name of .pgen/.bed file.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">\fB\-\-pvar\fR <filename></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">: Specify full name of .pvar/.bim file.</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.TP</span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">\fB\-\-psam\fR <filename></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">: Specify full name of .psam/.fam file.</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.TP</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">\fB\-\-bfile\fR</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"><prefix> ['vzs'] : Specify .bed + .bim[.zst] + .fam prefix.</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">\fB\-\-bpfile\fR <prefix> ['vzs'] : Specify .pgen + .bim[.zst] + .fam prefix.</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">\fB\-\-keep\-autoconv\fR ['vzs']</span>
</pre>
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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="plaintext">: When importing non\-PLINK\-binary data, don't</span>
</pre>
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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="plaintext">delete autogenerated fileset at end of run.</span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.TP</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">\fB\-\-no\-fid\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">: .fam file does not contain column 1 (family ID).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-no\-parents\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">: .fam file does not contain columns 3\-4 (parents).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-no\-sex\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">: .fam file does not contain column 5 (sex).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">\fB\-\-vcf\fR <filename> ['dosage='<field>]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-bcf\fR <filename> ['dosage='<field>] :</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">.IP</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">Specify full name of .vcf{|.gz|.zst} or BCF2 file to import.</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">* These can be used with \fB\-\-psam\fR/\-\-fam.</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">* By default, dosage information is not imported. To import the GP field</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.IP</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">(must be VCFv4.3\-style 0..1, one probability per possible genotype), add</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">\&'dosage=GP' (or 'dosage=GP\-force', see below). To import Minimac3\-style</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">for now) causes the named field to be interpreted as a Minimac3\-style</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">dosage.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">Note that, in the dosage=GP case, PLINK 2 collapses the probabilities</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">down to dosages; you cannot use PLINK 2 to losslessly convert VCF</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">FORMAT:GP data to e.g. BGEN format. To make this more obvious, PLINK 2</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">now errors out when dosage=GP is used on a file with a FORMAT:DS header</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">line and \fB\-\-import\-dosage\-certainty\fR wasn't specified, since dosage=DS</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">extracts the same information more quickly in this situation. You can</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">suppress this error with 'dosage=GP\-force'.</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">In all of these cases, hardcalls are regenerated from scratch from the</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">dosages. As a consequence, variants with no GT field can now be</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">imported; they will be assumed to contain only diploid calls when HDS is</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">also absent.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">.HP</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">\fB\-\-data\fR <filename prefix> <REF/ALT mode> ['gzs']</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">.HP</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">\fB\-\-bgen\fR <filename> <REF/ALT mode> ['snpid\-chr']</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.HP</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">\fB\-\-gen\fR <filename> <REF/ALT mode></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.HP</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">\fB\-\-sample\fR <filename> :</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.TP</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">Specify an Oxford\-format dataset to import.</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">\fB\-\-data\fR specifies a .gen[.zst]</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.IP</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">+ .sample pair, while \fB\-\-bgen\fR specifies a BGEN v1.1+ file.</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">* If a BGEN v1.2+ file contains sample IDs, it may be imported without a</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">.IP</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">companion .sample file.</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">* With 'snpid\-chr', chromosome codes are read from the 'SNP ID' field</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">.IP</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">instead of the usual chromosome field.</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">.IP</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">* The following REF/ALT modes are supported:</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">.IP</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">\&'ref\-first': The first allele for each variant is REF.</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">\&'ref\-last': The last allele for each variant is REF.</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">\&'ref\-unknown': The last allele for each variant is treated as</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.IP</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">provisional\-REF.</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">.HP</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">\fB\-\-haps\fR <filename> [{ref\-first | ref\-last}]</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.HP</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">\fB\-\-legend\fR <filename> <chr code> :</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">.IP</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">Specify .haps [+ .legend] file(s) to import.</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">* When \fB\-\-legend\fR is specified, it's assumed that the \fB\-\-haps\fR file doesn't</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">.IP</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">contain header columns.</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">.TP</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">* On chrX, the second male column may contain dummy '\-' entries.</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">(However,</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">.IP</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">PLINK 2 currently cannot handle omitted male columns.)</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">.IP</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">* If not used with \fB\-\-sample\fR, new sample IDs are of the form 'per#/per#'.</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">.TP</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">\fB\-\-map\fR <filename></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">: Specify full name of .map file.</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">.HP</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">\fB\-\-import\-dosage\fR <allele dosage file> ['noheader'] ['id\-delim='<char>]</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">.IP</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">['skip0='<i>] ['skip1='<j>] ['skip2='<k>] ['dose1']</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">['format='<m>] [{ref\-first | ref\-last}]</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">['single\-chr='<code>] ['chr\-col\-num='<#>]</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">['pos\-col\-num='<#>] :</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">.IP</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">Specify PLINK 1.x\-style dosage file to import.</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">* You must also specify a companion .psam/.fam file.</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">* By default, PLINK assumes that the file contains a header line, which has</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">.IP</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">\&'SNP' in (1\-based) column i+1, 'A1' in column i+j+2, 'A2' in column</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">normally zero, but can be changed with 'skip0', 'skip1', and 'skip2'</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">respectively. FID/IID are normally assumed to be separate tokens, but if</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">they're merged into a single token you can specify the delimiter with</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">\&'id\-delim='.) If such a header line is not present, use the 'noheader'</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">modifier; samples will then be assumed to appear in the same order as</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">they do in the .psam/.fam file.</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">.TP</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">* You may specify a companion .map file.</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">If you do not,</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">.IP</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">* 'single\-chr=' can be used to specify that all variants are on the named</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">.TP</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">chromosome.</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">Otherwise, you can use 'chr\-col\-num=' to read chromosome</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">.IP</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">codes from the given (1\-based) column number.</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">.IP</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">* 'pos\-col\-num=' causes bp coordinates to be read from the given column</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">.IP</span>
</pre>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">number.</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">.IP</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">* The 'format=' modifier lets you specify the number of values used to</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">.TP</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">represent each dosage.</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">\&'format=1' normally indicates a single 0..2 A1</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">.TP</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">expected count; 'dose1' modifies this to a 0..1 frequency.</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">\&'format=2'</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">.IP</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">likelihood. 'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2.</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">\&'format=infer' (the default) infers the format from the number of columns</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">in the first nonheader line.</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">.HP</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">\fB\-\-dummy\fR <sample ct> <SNP ct> [missing dosage freq] [missing pheno freq]</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">.IP</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">[{acgt | 1234 | 12}] ['pheno\-ct='<count>] ['scalar\-pheno']</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">['dosage\-freq='<rate>]</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">.IP</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">This generates a fake input dataset with the specified number of samples</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">and SNPs.</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">* By default, the missing dosage and phenotype frequencies are zero.</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">.IP</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">These can be changed by providing 3rd and 4th numeric arguments.</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">.IP</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">* By default, allele codes are As and Bs; this can be changed with the</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">.IP</span>
</pre>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">\&'acgt', '1234', or '12' modifier.</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">.TP</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">* By default, one binary phenotype is generated.</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">\&'pheno\-ct=' can be used</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">.IP</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">to change the number of phenotypes, and 'scalar\-pheno' causes these</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">phenotypes to be normally distributed scalars.</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">.TP</span>
</pre>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">* By default, all (nonmissing) dosages are in {0,1,2}.</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">To make some of</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">.TP</span>
</pre>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">them take on decimal values, use 'dosage\-freq='.</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">(These dosages are</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">.IP</span>
</pre>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">affected by \fB\-\-hard\-call\-threshold\fR and \fB\-\-dosage\-erase\-threshold\fR.)</span>
</pre>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">.TP</span>
</pre>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">\fB\-\-fa\fR <filename></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">: Specify full name of reference FASTA file.</span>
</pre>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">.PP</span>
</pre>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">Output files have names of the form 'plink2.<extension>' by default. You can</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">change the 'plink2' prefix with</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">\fB\-\-out\fR <prefix></span>
</pre>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">: Specify prefix for output files.</span>
</pre>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">.PP</span>
</pre>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">Most runs also require at least one of the following commands:</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">.HP</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">\fB\-\-rm\-dup\fR [mode] ['list']</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">.IP</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">Remove all but one instance of each duplicate\-ID variant (ignoring the</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">missing ID), and (with the 'list' modifier) write a list of duplicated IDs</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">to <output prefix>.rmdup.list.</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">The following modes of operation are supported:</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">* 'error' (default) causes this to error out when there's a genotype data</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">.TP</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">or other mismatch between the records.</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">A list of affected IDs is written</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">.IP</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">to <output prefix>.rmdup.mismatch.</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">.IP</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">* 'retain\-mismatch' causes all instances of a duplicate\-ID variant to be</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">.IP</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">retained when there's a genotype data or variant info mismatch; otherwise</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">one instance is kept. The .rmdup.mismatch file is also written.</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">.IP</span>
</pre>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">* 'exclude\-mismatch' removes all instances of duplicate\-ID mismatched</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">.IP</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">variants instead.</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">.IP</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">* 'exclude\-all' causes all instances of duplicate\-ID variants to be</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">.IP</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">removed, even when the actual records are identical.</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">.IP</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">* 'force\-first' causes only the first instance of duplicate\-ID variants to</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">.IP</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">be kept, under all circumstances.</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">.HP</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">\fB\-\-make\-pgen\fR ['vzs'] ['format='<code>] ['trim\-alts'] ['erase\-phase']</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">.IP</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">['erase\-dosage'] ['pvar\-cols='<col set descriptor>]</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">['psam\-cols='<col set descriptor>]</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">.HP</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">\fB\-\-make\-bpgen\fR ['vzs'] ['format='<code>] ['trim\-alts'] ['erase\-phase']</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">.IP</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">['erase\-dosage']</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">.HP</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">\fB\-\-make\-bed\fR ['vzs'] ['trim\-alts']</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">.IP</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">Create a new PLINK 2 binary fileset (\fB\-\-make\-pgen\fR = .pgen + .pvar[.zst] +</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">\&.psam, \fB\-\-make\-bpgen\fR = .pgen + .bim[.zst] + .fam).</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">* Unlike the automatic text\-to\-binary converters (which only heed</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">.IP</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">chromosome filters), this supports all of PLINK's filtering flags.</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">.IP</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">* The 'vzs' modifier causes the variant file (.pvar/.bim) to be</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">.IP</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">Zstd\-compressed.</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">.IP</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">* The 'format' modifier requests an uncompressed fixed\-variant\-width .pgen</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">.TP</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">file.</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">(These do not directly support multiallelic variants.) The</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">.IP</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">following format code is currently supported:</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">.IP</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">2: just like .bed, except with an extended (12\-byte instead of 3\-byte)</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">.IP</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">header containing variant/sample counts, and rotated genotype codes</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">(00 = hom ref, 01 = het, 10 = hom alt, 11 = missing).</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">.IP</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">* The 'erase\-phase' and 'erase\-dosage' modifiers prevent phase and dosage</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">.IP</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">information from being written to the new .pgen.</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">.IP</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">* The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT.</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">.IP</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">Supported optional .pvar column sets are:</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">.IP</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">xheader: All ## header lines (yeah, this is technically not a column),</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">.IP</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">except for possibly FILTER/INFO definitions when those</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">column(s) have been removed. Without this, only the #CHROM</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">header line is kept.</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">.IP</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">vcfheader: xheader, with additions to make it a valid VCF header.</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">maybequal: QUAL. Omitted if all remaining values are missing.</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">qual: Force QUAL column to be written even when empty.</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">maybefilter: FILTER. Omitted if all remaining values are missing.</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">filter: Force FILTER column to be written even when empty.</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">maybeinfo: INFO. Omitted if all remaining values are missing, or if</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">.IP</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">INFO:PR is the only subfield.</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">.IP</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">info: Force INFO column to be written.</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">maybecm: Centimorgan coordinate. Omitted if all remaining values = 0.</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">cm: Force CM column to be written even when empty.</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">.IP</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">The default is xheader,maybequal,maybefilter,maybeinfo,maybecm.</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">.IP</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">* Supported column sets for the .psam file are:</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">.TP</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">maybefid: Family ID, '0' = missing.</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">Omitted if all values missing.</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">.IP</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">fid: Force FID column to be written even when empty.</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">maybesid: Source ID, '0' = missing. Omitted if all values missing.</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">sid: Force SID column to be written even when empty.</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">maybeparents: Father and mother IIDs. Omitted if all values missing.</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">parents: Force PAT and MAT columns to be written even when empty.</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">sex: '1' = male, '2' = female, 'NA' = missing.</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">pheno1: First active phenotype. If none, all column entries are set to</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">.IP</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">the \fB\-\-output\-missing\-phenotype\fR string.</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">.TP</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext">phenos: All active phenotypes, if any.</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">(Can be combined with pheno1 to</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">.IP</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">force at least one phenotype column to be written.)</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">.IP</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">The default is maybefid,maybesid,maybeparents,sex,phenos.</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">.HP</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">\fB\-\-make\-just\-pvar\fR ['zs'] ['cols='<column set descriptor>]</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext">.HP</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">\fB\-\-make\-just\-psam\fR ['cols='<column set descriptor>]</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">.HP</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext">\fB\-\-make\-just\-bim\fR ['zs']</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">.HP</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">\fB\-\-make\-just\-fam\fR</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">.IP</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">Variants of \fB\-\-make\-pgen\fR/\-\-make\-bed which only write a new variant or sample</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext">file. These don't always require an input genotype file.</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext">USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">genotype data and your sample/variant indexes if you use these commands</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">improperly. If you have any doubt, stick with \fB\-\-make\-[b]pgen\fR/\-\-make\-bed.</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext">.HP</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext">\fB\-\-export\fR <output format(s)...> [{01 | 12}] ['bgz'] ['id\-delim='<char>]</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext">.IP</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">['id\-paste='<column set descriptor>] ['include\-alt']</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext">['omit\-nonmale\-y'] ['spaces'] ['vcf\-dosage='<field>] ['ref\-first']</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext">['bits='<#>]</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext">.TP</span>
</pre>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">Create a new fileset with all filters applied.</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext">The following output</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">.IP</span>
</pre>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">formats are supported:</span>
</pre>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">(actually, only A, AD, A\-transpose, bcf, bgen\-1.x, haps, hapslegend,</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext">ind\-major\-bed, oxford, and vcf are implemented for now)</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">* '23': 23andMe 4\-column format. This can only be used on a single</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">.IP</span>
</pre>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">sample's data (\fB\-\-keep\fR may be handy), and does not support</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext">multicharacter allele codes.</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">.IP</span>
</pre>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">* 'A': Sample\-major additive (0/1/2) coding, suitable for loading from R.</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">.IP</span>
</pre>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext">If you need uncounted alleles to be named in the header line, add</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">the 'include\-alt' modifier.</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">.IP</span>
</pre>
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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="plaintext">* 'AD': Sample\-major additive (0/1/2) + dominant (het=1/hom=0) coding.</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="plaintext">.IP</span>
</pre>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">Also supports 'include\-alt'.</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">.IP</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">* 'A\-transpose': Variant\-major 0/1/2.</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext">* 'beagle': Unphased per\-autosome .dat and .map files, readable by early</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext">.IP</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">BEAGLE versions.</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext">.IP</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext">* 'beagle\-nomap': Single .beagle.dat file.</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext">* 'bgen\-1.x': Oxford\-format .bgen + .sample. For v1.2/v1.3, sample</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext">.IP</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext">identifiers are stored in the .bgen (with id\-delim and</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext">id\-paste settings applied), and default precision is 16\-bit</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext">(use the 'bits' modifier to reduce this).</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext">.IP</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext">* 'bimbam': Regular BIMBAM format.</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext">* 'bimbam\-1chr': BIMBAM format, with a two\-column .pos.txt file. Does not</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext">.IP</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext">support multiple chromosomes.</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext">.IP</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext">* 'fastphase': Per\-chromosome fastPHASE files, with</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext">.IP</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext">\&.chr\-<chr #>.phase.inp filename extensions.</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext">.TP</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext">* 'fastphase\-1chr': Single .phase.inp file.</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext">Does not support</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">.IP</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext">multiple chromosomes.</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext">.TP</span>
</pre>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext">* 'haps', 'hapslegend': Oxford\-format .haps + .sample[ + .legend].</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext">All</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext">.TP</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext">data must be biallelic and phased.</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext">When the 'bgz'</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext">.TP</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext">modifier is present, the .haps file is</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext">block\-gzipped.</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext">.IP</span>
</pre>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext">* 'HV': Per\-chromosome Haploview files, with .chr\-<chr #>{.ped,.info}</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext">.IP</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext">filename extensions.</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext">.TP</span>
</pre>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext">* 'HV\-1chr': Single Haploview .ped + .info file pair.</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext">Does not support</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext">.IP</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext">multiple chromosomes.</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext">.IP</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext">* 'ind\-major\-bed': PLINK 1 sample\-major .bed (+ .bim + .fam).</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext">* 'lgen': PLINK 1 long\-format (.lgen + .fam + .map), loadable with \fB\-\-lfile\fR.</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext">* 'lgen\-ref': .lgen + .fam + .map + .ref, loadable with \fB\-\-lfile\fR +</span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext">.IP</span>
</pre>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext">\fB\-\-reference\fR.</span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext">* 'list': Single genotype\-based list, up to 4 lines per variant.</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext">To omit</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext">.IP</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext">nonmale genotypes on the Y chromosome, add the 'omit\-nonmale\-y'</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext">modifier.</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext">.IP</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">* 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext">.IP</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext">genotype\-based list which omits the most common genotype for</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext">each variant. Also supports 'omit\-nonmale\-y'.</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext">.TP</span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext">* 'oxford': Oxford\-format .gen + .sample.</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext">When the 'bgz' modifier is</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext">.IP</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext">present, the .gen file is block\-gzipped.</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext">.IP</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext">* 'ped': PLINK 1 sample\-major (.ped + .map), loadable with \fB\-\-file\fR.</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">* 'compound\-genotypes': Same as 'ped', except that the space between each</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext">.IP</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext">pair of same\-variant allele codes is removed.</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext">.IP</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext">* 'structure': Structure\-format.</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext">* 'transpose': PLINK 1 variant\-major (.tped + .tfam), loadable with</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext">.IP</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext">\fB\-\-tfile\fR.</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext">.TP</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext">* 'vcf',</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext">: VCF (default version 4.3). If PAR1 and PAR2 are present,</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext">.TP</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext">\&'vcf\-4.2',</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext">they are automatically merged with chrX, with proper</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext">.TP</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext">\&'bcf',</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext">handling of chromosome codes and male ploidy.</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext">.TP</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext">\&'bcf\-4.2'</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext">When the 'bgz' modifier is present, the VCF file is</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext">block\-gzipped. (This always happens with BCF output.)</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext">The 'id\-paste' modifier controls which .psam columns are</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext">used to construct sample IDs (choices are maybefid, fid,</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext">iid, maybesid, and sid; default is maybefid,iid,maybesid),</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">while the 'id\-delim' modifier sets the character between the</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext">ID pieces (default '_').</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext">Genotypes are always exported. If you want to export a</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext">sites\-only VCF instead, see \fB\-\-make\-pgen\fR/\-\-make\-just\-pvar's</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext">\&'vcfheader' column set.</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext">Dosages are not exported unless the 'vcf\-dosage=' modifier</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext">is present. The following five dosage export modes are</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext">supported:</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext">\&'GP': genotype posterior probabilities (v4.3 only).</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext">\&'DS': Minimac3\-style dosages, omitted for hardcalls.</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext">\&'DS\-force': Minimac3\-style dosages, never omit.</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext">\&'HDS': Minimac3\-style phased dosages, omitted for hardcalls</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext">.TP</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext">and unphased calls.</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext">Also includes 'DS' output.</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext">.IP</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext">\&'HDS\-force': Always report DS and HDS.</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext">.IP</span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext">In addition,</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext">* The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext">.IP</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext">to be coded as '2', while '01' maps alt1 \-> 0 and ref \-> 1.</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext">.IP</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="plaintext">* The 'spaces' modifier makes the output space\-delimited instead of</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext">.IP</span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="plaintext">tab\-delimited, whenever both are permitted.</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext">.IP</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="plaintext">* For biallelic formats where it's unspecified whether the reference/major</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext">.IP</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext">allele should appear first or second, \fB\-\-export\fR defaults to second for</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext">compatibility with PLINK 1.9. Use 'ref\-first' to change this.</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="plaintext">(Note that this doesn't apply to the 'A', 'AD', and 'A\-transpose'</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext">formats; use \fB\-\-export\-allele\fR to control which alleles are counted there.)</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext">.HP</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext">\fB\-\-freq\fR ['zs'] ['counts'] ['cols='<column set descriptor>] ['bins\-only']</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext">.IP</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext">['refbins='<comma\-separated bin boundaries> | 'refbins\-file='<file>]</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext">['alt1bins='<comma\-separated bin boundaries> | 'alt1bins\-file='<file>]</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext">.TP</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext">Empirical allele frequency report.</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext">By default, only founders are</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext">.TP</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext">considered.</span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext">Dosages are taken into account (e.g. heterozygous haploid</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext">.IP</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext">calls count as 0.5).</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext">Supported column sets are:</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext">.IP</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="plaintext">ref: Reference allele.</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext">reffreq: Reference allele frequency/dosage.</span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="plaintext">alt1freq: Alt1 frequency/dosage.</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext">altfreq: Comma\-separated frequencies/dosages for all alternate alleles.</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext">freq: Similar to altfreq, except ref is also included at the start.</span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext">eq: Comma\-separated <allele>=<freq> for all present alleles. (If no</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="plaintext">.IP</span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext">alleles are present, the column contains a single '.'.)</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="plaintext">eqz: Same as eq, except zero\-counts are included.</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="plaintext">alteq/alteqz: Same as eq/eqz, except reference allele is omitted.</span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="plaintext">numeq: 0=<freq>,1=<freq>, etc. Zero\-counts are omitted.</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="plaintext">altnumeq: Same as numeq, except reference allele is omitted.</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="plaintext">machr2: Unphased MaCH imputation quality metric.</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext">minimac3r2: Phased Minimac3 imputation quality.</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext">nobs: Number of allele observations.</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext">.IP</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext">The default is chrom,ref,alt,altfreq,nobs.</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="plaintext">Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext">\&'counts') file(s) are generated when 'refbins='/'refbins\-file=' or</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="plaintext">\&'alt1bins='/'alt1bins\-file=' is present; these report the total number of</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="plaintext">frequencies or counts in each left\-closed, right\-open interval. (If you</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext">only want these histogram(s), and not the main report, add 'bins\-only'.)</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="plaintext">.HP</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="plaintext">\fB\-\-geno\-counts\fR ['zs'] ['cols='<column set descriptor>]</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext">.IP</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="plaintext">Variant\-based hardcall genotype count report (considering both alleles</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext">simultaneously in the diploid case). Nonfounders are now included; use</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext">\fB\-\-keep\-founders\fR if this is a problem. Heterozygous haploid calls are</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext">treated as missing.</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="plaintext">Supported column sets are:</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext">.IP</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext">ref: Reference allele.</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="plaintext">homref: Homozygous\-ref count.</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext">refalt1: Heterozygous ref\-alt1 count.</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext">refalt: Comma\-separated het ref\-altx counts.</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext">homalt1: Homozygous\-alt1 count.</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="plaintext">altxy: Comma\-separated altx\-alty counts, in (1/1)\-(1/2)\-(2/2)\-(1/3)\-...</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="plaintext">.IP</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="plaintext">order.</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="plaintext">.IP</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="plaintext">xy: Similar to altxy, except the reference allele is treated as alt0,</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="plaintext">.IP</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="plaintext">and the sequence starts (0/0)\-(0/1)\-(1/1)\-(0/2)\-...</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext">.IP</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="plaintext">hapref: Haploid\-ref count.</span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="plaintext">hapalt1: Haploid\-alt1 count.</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="plaintext">hapalt: Comma\-separated haploid\-altx counts.</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="plaintext">hap: Similar to hapalts, except ref is also included at the start.</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="plaintext">numeq: 0/0=<hom ref ct>,0/1=<het ref\-alt1>,1/1=<hom alt1>,...,0=<hap ref></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext">.TP</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="plaintext">etc.</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="plaintext">Zero\-counts are omitted. (If all genotypes are missing, the</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="plaintext">.IP</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext">column contains a single '.'.)</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext">.IP</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext">missing: Number of missing genotypes.</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="plaintext">nobs: Number of (nonmissing) genotype observations.</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="plaintext">.IP</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext">The default is chrom,ref,alt,homref,refalt,altxy,hapref,hapalt,missing.</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="plaintext">.HP</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="plaintext">\fB\-\-sample\-counts\fR ['zs'] ['cols='<column set descriptor>]</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="plaintext">.IP</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext">Sample\-based hardcall genotype count report.</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext">* Unknown\-sex samples are treated as female.</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext">* Heterozygous haploid calls (MT included) are treated as missing.</span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext">* As with other PLINK 2 commands, SNPs that have not been left\-normalized</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="plaintext">.TP</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="plaintext">are counted as non\-SNP non\-symbolic.</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="plaintext">(Use e.g. \fB\-\-normalize\fR when that's a</span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="plaintext">.IP</span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="plaintext">problem.)</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="plaintext">.IP</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext">* Supported column sets are:</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext">.IP</span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="plaintext">maybefid: FID, if that column was present in the input.</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="plaintext">fid: Force FID column to be written even when absent in the input.</span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="plaintext">(IID is always present, and positioned here.)</span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="plaintext">maybesid: SID, if that column was present in the input.</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="plaintext">sid: Force SID column to be written even when absent in the input.</span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="plaintext">sex: '1' = male, '2' = female, 'NA' = missing.</span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="plaintext">hom: Homozygous genotype count.</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext">homref: Homozygous\-ref genotype count.</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="plaintext">homalt: Homozygous\-alt genotype count.</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext">homaltsnp: Homozygous\-alt SNP count.</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="plaintext">het: Heterozygous genotype count.</span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="plaintext">refalt: Heterozygous ref\-altx genotype count.</span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="plaintext">het2alt: Heterozygous altx\-alty genotype count.</span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="plaintext">hetsnp: Heterozygous SNP count.</span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="plaintext">dipts: Diploid SNP transition count.</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="plaintext">ts: SNP transition count (excluding chrY for females).</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext">diptv: Diploid SNP transversion count.</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext">tv: SNP transversion count.</span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext">dipnonsnpsymb: Diploid non\-SNP, non\-symbolic count.</span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext">nonsnpsymb: Non\-SNP, non\-symbolic count.</span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext">symbolic: Symbolic variant count.</span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext">nonsnp: Non\-SNP count.</span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext">dipsingle: Number of singletons relative to this dataset, across just</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext">.TP</span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext">diploid calls.</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext">(Note that if the ALT allele in a chrX</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext">.IP</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext">biallelic variant appears in exactly one female and one</span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext">male, that counts as a singleton for just the female.)</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext">.IP</span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext">single: Number of singletons relative to this dataset.</span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="plaintext">haprefwfemaley: Haploid\-ref count, counting chrY for everyone.</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="plaintext">hapref: Haploid\-ref count, excluding chrY for females.</span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="plaintext">hapaltwfemaley: Haploid\-alt count, counting chrY for everyone.</span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext">hapalt: Haploid\-alt count, excluding chrY for females.</span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext">missingwfemaley: Missing call count, counting chrY for everyone.</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="plaintext">missing: Missing call count, excluding chrY for females.</span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext">.IP</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext">The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv,</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext">dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley.</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext">.IP</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext">* The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb',</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext">\&'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous</span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext">altx\-alty call separately, since they can be of different subtypes.</span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext">(I.e. if they are of the same subtype, the corresponding count is</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext">incremented by 2.) As a consequence, these columns are unaffected by</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext">variant split/join.</span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="plaintext">\fB\-\-missing\fR ['zs'] [{sample\-only | variant\-only}]</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="plaintext">['scols='<column set descriptor>] ['vcols='<column set descriptor>]</span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="plaintext">.IP</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="plaintext">Generate sample\- and variant\-based missing data reports (or just one report</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="plaintext">if 'sample\-only'/'variant\-only' is specified).</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="plaintext">As of alpha 2, mixed MT hardcalls appear in the heterozygous haploid stats.</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="plaintext">Supported column sets in the sample\-based report are:</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="plaintext">.IP</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="plaintext">maybefid: FID, if that column was present in the input.</span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="plaintext">fid: Force FID column to be written even when absent in the input.</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext">(IID is always present, and positioned here.)</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="plaintext">maybesid: SID, if that column was present in the input.</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="plaintext">sid: Force SID column to be written even when absent in the input.</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="plaintext">misspheno1: First active phenotype missing (Y/N)? Always 'Y' if no</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="plaintext">.IP</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="plaintext">phenotypes are loaded.</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="plaintext">.TP</span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="plaintext">missphenos: A Y/N column for each loaded phenotype.</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="plaintext">(Can be combined</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="plaintext">.IP</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="plaintext">with misspheno1 to force at least one such column.)</span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="plaintext">nmissdosage: Number of missing dosages.</span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="plaintext">nmiss: Number of missing hardcalls, not counting het haploids.</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="plaintext">nmisshh: Number of missing hardcalls, counting het haploids.</span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="plaintext">hethap: Number of heterozygous haploid hardcalls.</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="plaintext">nobs: Denominator (male count on chrY, otherwise total sample count).</span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="plaintext">fmissdosage: Missing dosage rate.</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="plaintext">fmiss: Missing hardcall rate, not counting het haploids.</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="plaintext">fmisshh: Missing hardcall rate, counting het haploids.</span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="plaintext">.IP</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="plaintext">The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss.</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="plaintext">Supported column sets in the variant\-based report are:</span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="plaintext">.IP</span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="plaintext">ref: Reference allele.</span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="plaintext">nmissdosage: Number of missing dosages.</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="plaintext">nmiss: Number of missing hardcalls, not counting het haploids.</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext">nmisshh: Number of missing hardcalls, counting het haploids.</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="plaintext">hethap: Number of heterozygous haploid calls.</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="plaintext">nobs: Number of potentially valid calls.</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="plaintext">fmissdosage: Missing dosage rate.</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="plaintext">fmiss: Missing hardcall rate, not counting het haploids.</span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="plaintext">fmisshh: Missing hardcall rate, counting het haploids.</span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="plaintext">fhethap: Heterozygous haploid rate.</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="plaintext">.IP</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="plaintext">The default is chrom,nmiss,nobs,fmiss.</span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="plaintext">.HP</span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="plaintext">\fB\-\-hardy\fR ['zs'] ['midp'] ['redundant'] ['cols='<column set descriptor>]</span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="plaintext">.IP</span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="plaintext">Hardy\-Weinberg exact test p\-value report(s).</span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="plaintext">* By default, only founders are considered; change this with \fB\-\-nonfounders\fR.</span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="plaintext">* chrX is now omitted from the main <output prefix>.hardy report. Instead,</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="plaintext">.IP</span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="plaintext">(if present) it gets its own <output prefix>.hardy.x report based on the</span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="plaintext">method described in Graffelman J, Weir BS (2016) Hardy\-Weinberg</span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="plaintext">equilibrium and the X chromosome.</span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="plaintext">.IP</span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="plaintext">* For variants with k alleles where k>2, k separate 'biallelic' tests are</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="plaintext">.TP</span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="plaintext">performed, each reported on its own line.</span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="plaintext">However, biallelic variants</span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="plaintext">.IP</span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="plaintext">are normally reported on a single line, since the counts/frequencies</span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="plaintext">would be mirror\-images and the p\-values would be the same. You can add</span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="plaintext">the 'redundant' modifier to force biallelic variant results to be</span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="plaintext">reported on two lines for parsing convenience.</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="plaintext">.IP</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="plaintext">* There is currently no special handling of case/control phenotypes.</span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="plaintext">Supported column sets are:</span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="plaintext">.IP</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="plaintext">ref: Reference allele.</span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="plaintext">(A1 is always present, and positioned here.)</span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="plaintext">ax: Non\-A1 allele(s), comma\-separated.</span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="plaintext">gcounts: Hom\-A1 count, total number of het\-A1 calls, and total number of</span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="plaintext">.TP</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="plaintext">nonmissing calls with no copies of A1.</span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="plaintext">On chrX, these are</span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="plaintext">.IP</span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="plaintext">followed by male A1 and male non\-A1 counts.</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="plaintext">.IP</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="plaintext">gcount1col: gcounts values in a single comma\-separated column.</span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="plaintext">hetfreq: Observed and expected het\-A1 frequencies.</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="plaintext">sexaf: Female and male A1 observed allele frequencies (chrX only).</span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="plaintext">femalep: Female\-only p/midp\-value (chrX only).</span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="plaintext">p: Hardy\-Weinberg equilibrium exact test p/midp\-value.</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="plaintext">.IP</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="plaintext">The default is chrom,ax,gcounts,hetfreq,sexaf,p.</span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="plaintext">.HP</span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="plaintext">\fB\-\-indep\-pairwise\fR <window size>['kb'] [step size (variant ct)]</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="plaintext">.IP</span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="plaintext"><unphased\-hardcall\-r^2 threshold></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="plaintext">.IP</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="plaintext">Generate a list of variants in approximate linkage equilibrium.</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="plaintext">* For multiallelic variants, major allele counts are used in the r^2</span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="plaintext">.IP</span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="plaintext">computation.</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="plaintext">.IP</span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="plaintext">* With the 'kb' modifier, the window size is in kilobase instead of variant</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="plaintext">.TP</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="plaintext">count units.</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="plaintext">(Pre\-'kb' space is optional, i.e.</span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="plaintext">.IP</span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="plaintext">"\-\-indep\-pairwise 500 kb 0.5" and "\-\-indep\-pairwise 500kb 0.5" have the</span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="plaintext">same effect.)</span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="plaintext">.IP</span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="plaintext">* The step size now defaults to 1 if it's unspecified, and *must* be 1 if</span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="plaintext">.IP</span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="plaintext">the window is in kilobase units.</span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="plaintext">.IP</span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="plaintext">* Note that you need to rerun PLINK using \fB\-\-extract\fR or \fB\-\-exclude\fR on the</span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="plaintext">.IP</span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="plaintext">\&.prune.in/.prune.out file to apply the list to another computation... and</span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="plaintext">as with other applications of \fB\-\-extract\fR/\-\-exclude, duplicate variant IDs</span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="plaintext">are a problem. \fB\-\-indep\-pairwise\fR still runs to completion for now when</span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="plaintext">duplicate variant IDs are present, but that will become an error in alpha</span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="plaintext">3.</span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="plaintext">.HP</span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="plaintext">\fB\-\-ld\fR <variant ID> <variant ID> ['dosage'] ['hwe\-midp']</span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="plaintext">.IP</span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="plaintext">This displays diplotype frequencies, r^2, and D' for a single pair of</span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="plaintext">variants.</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="plaintext">* For multiallelic variants, major allele counts/dosages are used.</span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="plaintext">* Phase information is used when both variants are on the same chromosome.</span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="plaintext">* When there is at least one sample with unphased het calls for both</span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="plaintext">.IP</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="plaintext">variants, diplotype frequencies are estimated using the Hill equation.</span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="plaintext">If there are multiple biologically possible local maxima, all are</span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="plaintext">displayed, along with HWE exact test statistics.</span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="plaintext">.TP</span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="plaintext">* By default, only hardcalls are considered.</span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="plaintext">Add the 'dosage' modifier if</span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="plaintext">.TP</span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="plaintext">you want dosages to be taken into account.</span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="plaintext">(In the diploid case, an</span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="plaintext">.IP</span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="plaintext">unphased dosage of x is interpreted as P(0/0) = 1 \- x, P(0/1) = x when x</span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="plaintext">is in 0..1.)</span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="plaintext">.HP</span>
</pre>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="plaintext">\fB\-\-sample\-diff\fR ['id\-delim='<char>] ['dosage' | 'dosage='<tolerance>]</span>
</pre>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="plaintext">.IP</span>
</pre>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="plaintext">['include\-missing'] [{pairwise | counts\-only}]</span>
</pre>
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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="plaintext">['fname\-id\-delim='<c>] ['zs'] ['cols='<column set descriptor>]</span>
</pre>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="plaintext">['counts\-cols='<column set descriptor>]</span>
</pre>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="plaintext">{base= | ids=}<sample ID> [other sample ID(s)...]</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="plaintext">.HP</span>
</pre>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="plaintext">\fB\-\-sample\-diff\fR ['id\-delim='<char>] ['dosage' | 'dosage='<tolerance>]</span>
</pre>
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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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="plaintext">['include\-missing'] [{pairwise | counts\-only}]</span>
</pre>
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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="plaintext">['fname\-id\-delim='<c>] ['zs'] ['cols='<column set descriptor>]</span>
</pre>
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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="plaintext">['counts\-cols='<column set descriptor>] file=<ID\-pair file></span>
</pre>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="plaintext">.IP</span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="plaintext">(alias: \fB\-\-sdiff\fR)</span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="plaintext">Report discordances and discordance\-counts between pairs of samples. If</span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="plaintext">chrX or chrY is present, sex must be defined and consistent.</span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="plaintext">* There are three ways to specify which sample pairs to compare. To</span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="plaintext">.IP</span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="plaintext">compare a single baseline sample against some others, start the</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="plaintext">(space\-delimited) sample ID list with 'base='. To perform an all\-vs.\-all</span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="plaintext">comparison, start it with 'ids=' instead. To compare sample pairs listed</span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="plaintext">in a file, use 'file='.</span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="plaintext">Note that 'base='/'ids='/'file=' must be positioned after all modifiers.</span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="plaintext">.IP</span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="plaintext">* Sample IDs are interpreted as if they were in a VCF header line, with</span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="plaintext">.IP</span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="plaintext">\&'id\-delim=' having the usual effect.</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="plaintext">.TP</span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="plaintext">* By default, comparisons are based on hardcalls.</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="plaintext">Use 'dosage' to compare</span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="plaintext">.IP</span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="plaintext">dosages instead; you can combine this with a tolerance in [0, 0.5).</span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="plaintext">.IP</span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="plaintext">* By default, if one genotype is missing and the other isn't, that doesn't</span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="plaintext">.IP</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="plaintext">count as a difference; this can be changed with 'include\-missing'.</span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="plaintext">.IP</span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="plaintext">* By default, a single main report is written to</span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="plaintext">.TP</span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="plaintext"><output prefix>[.<base ID>].sdiff.</span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="plaintext">To write separate pairwise</span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="plaintext">.IP</span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="plaintext"><output prefix>.<ID1>.<ID2>.sdiff reports for each compared ID pair, add</span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="plaintext">the 'pairwise' modifier. To omit the main report, add the 'counts\-only'</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="plaintext">modifier. (Note that, if you're only interested in nonmissing autosomal</span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="plaintext">biallelic hardcalls, \fB\-\-make\-king\-table\fR provides a more efficient way to</span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="plaintext">compute just counts.)</span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="plaintext">.IP</span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="plaintext">* By default, if an output filename has a multipart sample ID, the parts</span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="plaintext">.IP</span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="plaintext">will be delimited by '_'; use 'fname\-id\-delim=' to change this.</span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="plaintext">.IP</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="plaintext">Supported main\-report column sets are:</span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="plaintext">.IP</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="plaintext">(Variant ID is always present, and positioned here.)</span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="plaintext">ref: Reference allele.</span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="plaintext">maybefid: FID1/FID2, if that column was in the input. Requires 'id'.</span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="plaintext">fid: Force FID1/FID2 even when FID was absent in the input.</span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="plaintext">id: IID1/IID2.</span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="plaintext">maybesid: SID1/SID2, if that column was in the input. Requires 'id'.</span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="plaintext">sid: Force SID1/SID2 even when SID was absent in the input.</span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="plaintext">geno: Unphased GT or DS for the two samples.</span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="plaintext">.IP</span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="plaintext">The default is usually chrom,pos,ref,alt,maybefid,id,maybesid,geno; the</span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="plaintext">sample IDs are removed from the default in 'pairwise' mode.</span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="plaintext">Supported discordance\-count\-summary column sets are:</span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="plaintext">.IP</span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="plaintext">maybefid: FID1/FID2, if that column was in the input.</span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="plaintext">fid: Force FID1/FID2 even when FID was absent in the input.</span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="plaintext">(IID1/IID2 are always present.)</span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="plaintext">maybesid: SID1/SID2, if that column was in the input.</span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="plaintext">sid: Force SID1/SID2 even when SID was absent in the input.</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="plaintext">nobs: Number of variants considered. This includes variants where one or</span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="plaintext">.IP</span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="plaintext">both variants are missing iff 'include\-missing' was specified.</span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="plaintext">.IP</span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="plaintext">nobsibs: ibs0+ibs1+ibs2.</span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="plaintext">ibs0: Number of diploid variants with no common hardcall alleles.</span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="plaintext">ibs1: Number of diploid variants with exactly 1 common hardcall allele.</span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="plaintext">ibs2: Number of diploid variants with both hardcall alleles matching.</span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="plaintext">halfmiss: Number of variants with exactly 1 missing genotype/dosage.</span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="plaintext">.IP</span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="plaintext">Ignored without 'include\-missing'.</span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="plaintext">.IP</span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="plaintext">diff: Total number of differences.</span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="plaintext">.IP</span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="plaintext">The default is maybefid,maybesid,nobs,halfmiss,diff.</span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="plaintext">.HP</span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="plaintext">\fB\-\-make\-king\fR [{square | square0 | triangle}] [{zs | bin | bin4}]</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="plaintext">.IP</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="plaintext">KING\-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC,</span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="plaintext">Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in</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="plaintext">genome\-wide association studies. By default, this writes a</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="plaintext">lower\-triangular tab\-delimited table of kinship coefficients to</span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="plaintext"><output prefix>.king, and a list of the corresponding sample IDs to</span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="plaintext"><output prefix>.king.id. The first row of the .king file contains a single</span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="plaintext"><genome 1\-genome 2> kinship coefficient, the second row has the</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="plaintext"><genome 1\-genome 3> and <genome 2\-genome 3> kinship values in that order,</span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="plaintext">etc.</span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="plaintext">* Only autosomes are currently considered.</span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="plaintext">* Pedigree information is currently ignored; the between\-family estimator</span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="plaintext">.IP</span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="plaintext">is used for all pairs.</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="plaintext">.IP</span>
</pre>
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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="plaintext">* For multiallelic variants, REF allele counts are used.</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="plaintext">* If the 'square' or 'square0' modifier is present, a square matrix is</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="plaintext">.IP</span>
</pre>
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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="plaintext">written instead; 'square0' fills the upper right triangle with zeroes.</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="plaintext">.IP</span>
</pre>
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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="plaintext">* If the 'zs' modifier is present, the .king file is Zstd\-compressed.</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="plaintext">* If the 'bin' modifier is present, a binary (square) matrix of</span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="plaintext">.IP</span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="plaintext">double\-precision floating point values, suitable for loading from R, is</span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="plaintext">instead written to <output prefix>.king.bin. ('bin4' specifies</span>
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<td class="diff-line-num new new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="plaintext">single\-precision numbers instead.) This can be combined with 'square0'</span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="plaintext">if you still want the upper right zeroed out, or 'triangle' if you don't</span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="plaintext">want to pad the upper right at all.</span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="plaintext">.IP</span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="plaintext">* The computation can be subdivided with \fB\-\-parallel\fR.</span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="plaintext">.HP</span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="plaintext">\fB\-\-make\-king\-table\fR ['zs'] ['counts'] ['rel\-check'] ['cols='<col set descrip.>]</span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="plaintext">.IP</span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="plaintext">Similar to \fB\-\-make\-king\fR, except results are reported in KING's original</span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="plaintext">\&.kin0 text table format (with minor changes, e.g. row order is more</span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="plaintext">friendly to incremental addition of samples), \fB\-\-king\-table\-filter\fR can be</span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="plaintext">used to restrict the report to high kinship values, and the 'rel\-check'</span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="plaintext">modifier can be used to restrict to same\-FID pairs.</span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="plaintext">Supported column sets are:</span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="plaintext">.TP</span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="plaintext">maybefid: FID1/FID2, if that column was in the input.</span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="plaintext">Requires 'id'.</span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="plaintext">.IP</span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="plaintext">fid: Force FID1/FID2 even when FID was absent in the input.</span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="plaintext">id: IID1/IID2.</span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="plaintext">maybesid: SID1/SID2, if that column was in the input. Requires 'id'.</span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="plaintext">sid: Force SID1/SID2 even when SID was absent in the input.</span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="plaintext">nsnp: Number of variants considered (autosomal, neither call missing).</span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="plaintext">hethet: Proportion/count of considered call pairs which are het\-het.</span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="plaintext">ibs0: Proportion/count of considered call pairs which are opposite homs.</span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="plaintext">ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts.</span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="plaintext">kinship: KING\-robust between\-family kinship estimator.</span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="plaintext">.IP</span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="plaintext">The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship.</span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="plaintext">hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is</span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="plaintext">present. If id is omitted, a .kin0.id file is also written.</span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="plaintext">.HP</span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="plaintext">\fB\-\-make\-rel\fR ['cov'] ['meanimpute'] [{square | square0 | triangle}]</span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="plaintext">.IP</span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="plaintext">[{zs | bin | bin4}]</span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="plaintext">.IP</span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="plaintext">Write a lower\-triangular variance\-standardized relationship matrix to</span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="plaintext"><output prefix>.rel, and corresponding IDs to <output prefix>.rel.id.</span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="plaintext">* This computation assumes that variants do not have very low MAF, or</span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="plaintext">.IP</span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="plaintext">deviate greatly from Hardy\-Weinberg equilibrium.</span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="plaintext">.IP</span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="plaintext">* Also, it's usually best to perform this calculation on a variant set in</span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="plaintext">.IP</span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="plaintext">approximate linkage equilibrium.</span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="plaintext">.IP</span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="plaintext">* The 'cov' modifier replaces the variance\-standardization step with basic</span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="plaintext">.IP</span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="plaintext">mean\-centering, causing a covariance matrix to be calculated instead.</span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="plaintext">.IP</span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="plaintext">* The computation can be subdivided with \fB\-\-parallel\fR.</span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="plaintext">.HP</span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="plaintext">\fB\-\-make\-grm\-list\fR ['cov'] ['meanimpute'] ['zs'] [{id\-header | iid\-only}]</span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="plaintext">.HP</span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="plaintext">\fB\-\-make\-grm\-bin\fR ['cov'] ['meanimpute'] [{id\-header | iid\-only}]</span>
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993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="plaintext">.HP</span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="plaintext">\fB\-\-make\-grm\-list\fR causes the relationships to be written to GCTA's original</span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="plaintext">.IP</span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="plaintext">list format, which describes one pair per line, while \fB\-\-make\-grm\-bin\fR writes</span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="plaintext">them in GCTA 1.1+'s single\-precision triangular binary format. Note that</span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="plaintext">these formats explicitly report the number of valid observations (where</span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="plaintext">neither sample has a missing call) for each pair, which is useful input for</span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="plaintext">some scripts.</span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="plaintext">.HP</span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="plaintext">\fB\-\-pca\fR [count] [{approx | meanimpute}] ['scols='<col set descriptor>]</span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="plaintext">.HP</span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="plaintext">\fB\-\-pca\fR [{allele\-wts | biallelic\-var\-wts}] [count] [{approx | meanimpute}]</span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="plaintext">.IP</span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="plaintext">['vzs'] ['scols='<col set descriptor>] ['vcols='<col set descriptor>]</span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="plaintext">.IP</span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="plaintext">Extracts top principal components from the variance\-standardized</span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="plaintext">relationship matrix.</span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="plaintext">* It is usually best to perform this calculation on a variant set in</span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="plaintext">.IP</span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="plaintext">approximate linkage equilibrium, with no very\-low\-MAF variants.</span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="plaintext">.IP</span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="plaintext">* By default, 10 PCs are extracted; you can adjust this by passing a</span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="plaintext">.TP</span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="plaintext">numeric argument.</span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="plaintext">(Note that 10 is lower than the PLINK 1.9 default of</span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="plaintext">.IP</span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="plaintext">20; this is due to the randomized algorithm's memory footprint growing</span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="plaintext">quadratically w.r.t. the PC count.)</span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="plaintext">.IP</span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="plaintext">* The 'approx' modifier causes the standard deterministic computation to be</span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="plaintext">.IP</span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="plaintext">replaced with the randomized algorithm originally implemented for</span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="plaintext">Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ,</span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="plaintext">Price AL (2016) Fast Principal\-Component Analysis Reveals Convergent</span>
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1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="plaintext">Evolution of ADH1B in Europe and East Asia. This can be a good idea when</span>
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1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="plaintext">you have >5k samples, and is almost required with >50k.</span>
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1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="plaintext">.IP</span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="plaintext">* The randomized algorithm always uses mean imputation for missing genotype</span>
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1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="plaintext">.TP</span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="plaintext">calls.</span>
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1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="plaintext">For comparison purposes, you can use the 'meanimpute' modifier to</span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="plaintext">.IP</span>
</pre>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="plaintext">request this behavior for the standard computation.</span>
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1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="plaintext">.IP</span>
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1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="plaintext">* 'scols=' can be used to customize how sample IDs appear in the .eigenvec</span>
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1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="plaintext">.TP</span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="plaintext">file.</span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="plaintext">(maybefid, fid, maybesid, and sid supported; default is</span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="plaintext">.IP</span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="plaintext">maybefid,maybesid.)</span>
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1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="plaintext">.IP</span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="plaintext">* The 'allele\-wts' modifier requests an additional one\-line\-per\-allele</span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="plaintext">.IP</span>
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1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="plaintext">\&.eigenvec.allele file with PCs expressed as allele weights instead of</span>
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1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="plaintext">sample weights. When it's present, 'vzs' causes the .eigenvec.allele</span>
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1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="plaintext">file to be Zstd\-compressed.</span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="plaintext">\&'vcols=' can be used to customize the report columns; supported column</span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="plaintext">sets are:</span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="plaintext">.IP</span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="plaintext">ref: Reference allele.</span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="plaintext">(A1 is always present, and positioned here.)</span>
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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="plaintext">ax: Non\-A1 alleles, comma\-separated.</span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="plaintext">(PCs are always present, and positioned here.)</span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="plaintext">.IP</span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="plaintext">Default is chrom,ref,alt.</span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="plaintext">.IP</span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="plaintext">* For datasets with no multiallelic variants, the 'biallelic\-var\-wts'</span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="plaintext">.IP</span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="plaintext">modifier requests the old .eigenvec.var format, which only reports</span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="plaintext">weights for major alleles. (These weights are 2x the corresponding</span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="plaintext">\&.eigenvec.allele weights.) Supported column sets are:</span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="plaintext">.IP</span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="plaintext">ref: Reference allele.</span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="plaintext">maj: Major allele.</span>
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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="plaintext">nonmaj: Minor allele.</span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="plaintext">(PCs are always present, and positioned here. Signs are w.r.t. the</span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="plaintext">major, not necessarily reference, allele.)</span>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="plaintext">.IP</span>
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1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="plaintext">Default is chrom,maj,nonmaj.</span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="plaintext">.HP</span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="plaintext">\fB\-\-king\-cutoff\fR [.king.bin + .king.id fileset prefix] <threshold></span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="plaintext">.IP</span>
</pre>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="plaintext">Exclude one member of each pair of samples with KING\-robust kinship greater</span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="plaintext">than the given threshold. Remaining/excluded sample IDs are written to</span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="plaintext"><output prefix>.king.cutoff.in.id + .king.cutoff.out.id.</span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="plaintext">If present, the .king.bin file must be triangular (either precision is ok).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="plaintext">\fB\-\-write\-covar\fR ['cols='<column set descriptor>]</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="plaintext">.IP</span>
</pre>
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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="plaintext">If covariates are defined, an updated version (with all filters applied) is</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="plaintext">automatically written to <output prefix>.cov whenever \fB\-\-make\-pgen\fR,</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="plaintext">\fB\-\-make\-just\-psam\fR, \fB\-\-export\fR, or a similar command is present. However, if</span>
</pre>
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</td>
<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="plaintext">you do not wish to simultaneously generate a new sample file, you can use</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="plaintext">\fB\-\-write\-covar\fR to just produce a pruned covariate file.</span>
</pre>
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</td>
<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="plaintext">Supported column sets are:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="plaintext">maybefid: FID, if that column was in the input.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="plaintext">fid: Force FID column to be written even when absent in the input.</span>
</pre>
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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="plaintext">maybesid: SID, if that column was in the input.</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="plaintext">sid: Force SID column to be written even when absent in the input.</span>
</pre>
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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="plaintext">maybeparents: Father/mother IIDs ('0' = missing), if columns in input.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">parents: Force PAT/MAT columns to be written even when absent in input.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">sex: '1' = male, '2' = female, 'NA' = missing.</span>
</pre>
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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="plaintext">pheno1: First active phenotype. If none, all column entries are set to</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="plaintext">the \fB\-\-output\-missing\-phenotype\fR string.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="plaintext">phenos: All active phenotypes, if any.</span>
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<td class="diff-line-num new new_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="plaintext">(Can be combined with pheno1 to</span>
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<td class="diff-line-num new new_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="plaintext">force at least one phenotype column to be written.)</span>
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<td class="diff-line-num new new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="plaintext">(Covariates are always present, and positioned here.)</span>
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<td class="diff-line-num new new_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="plaintext">The default is maybefid,maybesid.</span>
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<td class="diff-line-num new new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="plaintext">\fB\-\-write\-samples\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="plaintext">Report IDs of all samples which pass your filters/inclusion thresholds.</span>
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<td class="diff-line-num new new_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="plaintext">\fB\-\-write\-snplist\fR ['zs'] ['allow\-dups']</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="plaintext">List all variants which pass your filters/inclusion thresholds.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="plaintext">Unless the</span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="plaintext">\&'allow\-dups' modifier is provided, this now errors out when duplicate</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="plaintext">variant ID(s) remain.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="plaintext">\fB\-\-glm\fR ['zs'] ['omit\-ref'] [{sex | no\-x\-sex}] ['log10'] ['pheno\-ids']</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="plaintext">[{genotypic | hethom | dominant | recessive}] ['interaction'] ['skip']</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="plaintext">['hide\-covar'] [{no\-firth | firth\-fallback | firth}] ['intercept']</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="plaintext">['cols='<col set desc>] ['local\-covar='<file>] ['local\-psam='<file>]</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="plaintext">['local\-pos\-cols='<key col #s> | 'local\-pvar='<file>] ['local\-haps']</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="plaintext">['local\-omit\-last' | 'local\-cats[0]='<category ct>] ['allow\-no\-covars']</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="plaintext">.IP</span>
</pre>
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1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="plaintext">Basic association analysis on quantitative and/or case/control phenotypes.</span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="plaintext">For each variant, a linear (for quantitative traits) or logistic (for</span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="plaintext">case/control) regression is run with the phenotype as the dependent</span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="plaintext">variable, and nonmajor allele dosage(s) and a constant\-1 column as</span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="plaintext">predictors.</span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="plaintext">* There is usually an additive effect line for every nonmajor allele, and</span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="plaintext">.TP</span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="plaintext">no such line for the major allele.</span>
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1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="plaintext">To omit REF alleles instead of major</span>
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1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="plaintext">.TP</span>
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1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="plaintext">alleles, add the 'omit\-ref' modifier.</span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="plaintext">(When performing interaction</span>
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1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="plaintext">.IP</span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="plaintext">testing, this tends to cause the multicollinearity check to fail for</span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="plaintext">low\-ref\-frequency variants.)</span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="plaintext">.IP</span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="plaintext">* By default, sex (male = 1, female = 2; note that this is a change from</span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="plaintext">.IP</span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="plaintext">PLINK 1.x) is automatically added as a predictor for X chromosome</span>
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1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="plaintext">variants, and no others. The 'sex' modifier causes it to be added</span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="plaintext">everywhere (except chrY), while 'no\-x\-sex' excludes it entirely.</span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="plaintext">.IP</span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="plaintext">* The 'log10' modifier causes p\-values to be reported in \fB\-log10\fR(p) form.</span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="plaintext">* 'pheno\-ids' causes the samples used in each set of regressions to be</span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="plaintext">.TP</span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="plaintext">written to an .id file.</span>
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1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="plaintext">(When the samples differ on chrX or chrY, .x.id</span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="plaintext">.IP</span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="plaintext">and/or .y.id files are also written.)</span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="plaintext">.IP</span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="plaintext">* The 'genotypic' modifier adds an additive effect/dominance deviation 2df</span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="plaintext">.IP</span>
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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="plaintext">joint test (0\-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and</span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="plaintext">0..1..0 coding instead.</span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="plaintext">.IP</span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="plaintext">* 'dominant' and 'recessive' specify a model assuming full dominance or</span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="plaintext">.TP</span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="plaintext">recessiveness, respectively, for the ref allele.</span>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="plaintext">I.e. the genotype</span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="plaintext">.IP</span>
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1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="plaintext">column is recoded as 0..1..1 or 0..0..1, respectively.</span>
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1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="plaintext">.TP</span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="plaintext">* 'interaction' adds genotype x covariate interactions to the model.</span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="plaintext">Note</span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="plaintext">.IP</span>
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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="plaintext">that this tends to produce 'NA' results (due to the multicollinearity</span>
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1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="plaintext">check) when the reference allele is 'wrong'; \fB\-\-maj\-ref\fR can be used to</span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="plaintext">enable analysis of those variants.</span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="plaintext">.TP</span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="plaintext">* Additional predictors can be added with \fB\-\-covar\fR.</span>
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1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="plaintext">By default, association</span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="plaintext">.IP</span>
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1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="plaintext">statistics are reported for all nonconstant predictors; 'hide\-covar'</span>
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1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="plaintext">suppresses covariate\-only results, while 'intercept' causes intercepts</span>
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1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="plaintext">to be reported.</span>
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1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="plaintext">Since running \fB\-\-glm\fR without at least e.g. principal component covariates</span>
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1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="plaintext">is usually an analytical mistake, the 'allow\-no\-covars' modifier is now</span>
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1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="plaintext">required when you're intentionally running \fB\-\-glm\fR without a covariate</span>
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1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="plaintext">file.</span>
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1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="plaintext">.IP</span>
</pre>
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1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="plaintext">* By default, if the current phenotype and covariates are such that every</span>
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1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="plaintext">.TP</span>
</pre>
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1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="plaintext">regression on a chromosome will fail, PLINK 2 errors out.</span>
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1202
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="plaintext">To just skip</span>
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1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="plaintext">.IP</span>
</pre>
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1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="plaintext">the phenotype or chromosome instead, add the 'skip' modifier.</span>
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<td class="diff-line-num new new_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="plaintext">* There are now three regression modes for case/control phenotypes:</span>
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1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="plaintext">* 'no\-firth' requests PLINK 1.x's behavior, where a NA result is reported</span>
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<td class="diff-line-num new new_line" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="plaintext">when basic logistic regression fails to converge.</span>
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<td class="diff-line-num new new_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="plaintext">.IP</span>
</pre>
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1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="plaintext">* 'firth\-fallback' requests logistic regression, followed by Firth</span>
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<td class="diff-line-num new new_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="plaintext">regression whenever the logistic regression fails to converge.</span>
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1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="plaintext">This is</span>
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<td class="diff-line-num new new_line" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1217
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="plaintext">now the default.</span>
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<td class="diff-line-num new new_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="plaintext">* 'firth' requests Firth regression all the time.</span>
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1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="plaintext">* To add covariates which are not constant across all variants, add the</span>
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<td class="diff-line-num new new_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1222
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1223
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="plaintext">\&'local\-covar=' and 'local\-psam=' modifiers, use full filenames for each,</span>
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<td class="diff-line-num new new_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1224
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="plaintext">and use either 'local\-pvar=' or 'local\-pos\-cols=' to provide variant ID</span>
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<td class="diff-line-num new new_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="plaintext">or position information.</span>
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<td class="diff-line-num new new_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="plaintext">Normally, the local\-covar file should have c * n real\-valued columns,</span>
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1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="plaintext">where the first c columns correspond to the first sample in the</span>
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1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="plaintext">local\-psam file, columns (c+1) to 2c correspond to the second sample,</span>
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1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="plaintext">etc.; and the mth line corresponds to the mth nonheader line of the</span>
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1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="plaintext">local\-pvar file when there is one. (Variants outside of the local\-pvar</span>
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<td class="diff-line-num new new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="plaintext">file are excluded from the regression.) The local covariates are</span>
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<td class="diff-line-num new new_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="plaintext">assigned the names LOCAL1, LOCAL2, etc.; to exclude the last local</span>
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<td class="diff-line-num new new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="plaintext">covariate from the regression (necessary if they are e.g. local ancestry</span>
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<td class="diff-line-num new new_line" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="plaintext">coefficients which sum to 1), add 'local\-omit\-last'.</span>
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<td class="diff-line-num new new_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="plaintext">Alternatively, with 'local\-cats='<k>, the local\-covar file is expected to</span>
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<td class="diff-line-num new new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="plaintext">have n columns with integer\-valued entries in [1, k]. (This range is</span>
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<td class="diff-line-num new new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="plaintext">[0, k\-1] with 'local\-cats0='.) These category assignments are expanded</span>
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1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="plaintext">into (k\-1) local covariates in the usual manner.</span>
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<td class="diff-line-num new new_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="plaintext">When position information is in the local\-covar file, this should be</span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="plaintext">indicated by 'local\-pos\-cols='<number of header rows>,<chrom col #>,<pos</span>
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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="plaintext">start col #>,<first covariate col #>.</span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="plaintext">\&'local\-haps' indicates that there's one column or column\-group per</span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="plaintext">haplotype instead of per sample; they are averaged by \fB\-\-glm\fR.</span>
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1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="plaintext">.IP</span>
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1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="plaintext">The main report supports the following column sets:</span>
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1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="plaintext">.IP</span>
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1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="plaintext">ref: Reference allele.</span>
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1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="plaintext">(A1 is always present, and positioned here. For multiallelic variants,</span>
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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="plaintext">this column may contain multiple comma\-separated alleles when the result</span>
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1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="plaintext">doesn't depend on which allele is A1.)</span>
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1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="plaintext">ax: Non\-A1 alleles, comma\-separated.</span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="plaintext">a1count: A1 allele count (can be decimal with dosage data).</span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="plaintext">totallele: Allele observation count (can be higher than \fB\-\-freq\fR value, due</span>
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1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="plaintext">.IP</span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="plaintext">to inclusion of het haploids and chrX model).</span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="plaintext">.IP</span>
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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="plaintext">a1countcc: A1 count in cases, then controls (case/control only).</span>
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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="plaintext">totallelecc: Case and control allele observation counts.</span>
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1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="plaintext">gcountcc: Genotype hardcall counts (neither\-A1, het\-A1, A1\-A1) in cases,</span>
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1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="plaintext">.IP</span>
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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="plaintext">then controls (case/control only).</span>
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1267
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="plaintext">.IP</span>
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1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="plaintext">a1freq: A1 allele frequency.</span>
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1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="plaintext">a1freqcc: A1 frequency in cases, then controls (case/control only).</span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="plaintext">machr2: Unphased MaCH imputation quality (frequently labeled 'INFO').</span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="plaintext">firth: Reports whether Firth regression was used (firth\-fallback only).</span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="plaintext">test: Test identifier. (Required unless only one test is run.)</span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="plaintext">nobs: Number of samples in the regression.</span>
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1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="plaintext">beta: Regression coefficient (for A1 if additive test).</span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="plaintext">orbeta: Odds ratio for case/control, beta for quantitative traits.</span>
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1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="plaintext">.IP</span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="plaintext">(Ignored if 'beta' column set included.)</span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="plaintext">.IP</span>
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1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="plaintext">se: Standard error of beta.</span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="plaintext">ci: Bounds of symmetric approximate confidence interval (requires \fB\-\-ci\fR).</span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="plaintext">tz: T\-statistic for linear regression, Wald Z\-score for logistic/Firth.</span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="plaintext">p: Asymptotic p\-value (or \fB\-log10\fR(p)) for T/Z\-statistic.</span>
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1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="plaintext">err: Error code for NA results.</span>
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1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="plaintext">.IP</span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="plaintext">The default is chrom,pos,ref,alt,firth,test,nobs,orbeta,se,ci,tz,p,err.</span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="plaintext">.HP</span>
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1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="plaintext">\fB\-\-score\fR <filename> [i] [j] [k] [{header | header\-read}]</span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="plaintext">.IP</span>
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1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="plaintext">[{center | variance\-standardize | dominant | recessive}]</span>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="plaintext">['no\-mean\-imputation'] ['se'] ['zs'] ['ignore\-dup\-ids']</span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="plaintext">[{list\-variants | list\-variants\-zs}] ['cols='<col set descriptor>]</span>
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1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="plaintext">.IP</span>
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1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="plaintext">Apply linear scoring system(s) to each sample.</span>
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1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="plaintext">The input file should have one line per scored (variant, allele) pair.</span>
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1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="plaintext">Variant IDs are read from column #i and allele codes are read from column</span>
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1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="plaintext">#j, where i defaults to 1 and j defaults to i+1.</span>
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1297
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="plaintext">* By default, a single column of input coefficients is read from column #k,</span>
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1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="plaintext">.TP</span>
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1299
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="plaintext">where k defaults to j+1.</span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="plaintext">(\fB\-\-score\-col\-nums\fR can be used to specify</span>
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1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="plaintext">.IP</span>
</pre>
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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="plaintext">multiple columns.)</span>
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1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="plaintext">.IP</span>
</pre>
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1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="plaintext">* 'header\-read' causes the first line of the input file to be treated as a</span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="plaintext">.TP</span>
</pre>
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1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="plaintext">header line containing score names.</span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="plaintext">Otherwise, score(s) are assigned the</span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="plaintext">.IP</span>
</pre>
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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="plaintext">names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line</span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="plaintext">to be entirely ignored.</span>
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1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="plaintext">.IP</span>
</pre>
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1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="plaintext">* By default, copies of unnamed alleles contribute zero to score, while</span>
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1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="plaintext">.IP</span>
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1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="plaintext">missing genotypes contribute an amount proportional to the loaded (via</span>
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1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="plaintext">\fB\-\-read\-freq\fR) or imputed allele frequency. To throw out missing</span>
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1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="plaintext">observations instead (decreasing the denominator in the final average</span>
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<td class="diff-line-num new new_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="plaintext">when this happens), use the 'no\-mean\-imputation' modifier.</span>
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1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="plaintext">.IP</span>
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1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="plaintext">* You can use the 'center' modifier to shift all genotypes to mean zero, or</span>
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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="plaintext">.IP</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="plaintext">\&'variance\-standardize' to linearly transform the genotypes to mean\-0,</span>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="plaintext">variance\-1.</span>
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1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="plaintext">* The 'dominant' modifier causes dosages greater than 1 to be treated as 1,</span>
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1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="plaintext">.IP</span>
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1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="plaintext">while 'recessive' uses max(dosage \- 1, 0) on diploid chromosomes.</span>
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1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="plaintext">('dominant', 'recessive', and 'variance\-standardize' cannot be used with</span>
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1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="plaintext">chrX.)</span>
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1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="plaintext">.IP</span>
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1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="plaintext">* The 'se' modifier causes the input coefficients to be treated as</span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="plaintext">.IP</span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="plaintext">independent standard errors; in this case, standard errors for the score</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="plaintext">average/sum are reported. (Note that this will systematically</span>
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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="plaintext">underestimate standard errors when scored variants are in LD.)</span>
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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="plaintext">.IP</span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="plaintext">* By default, \fB\-\-score\fR errors out if a variant ID in the input file appears</span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="plaintext">.TP</span>
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1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="plaintext">multiple times in the main dataset.</span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="plaintext">Use the 'ignore\-dup\-ids' modifier to</span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="plaintext">.IP</span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="plaintext">skip them instead (a warning is still printed if such variants are</span>
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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="plaintext">present).</span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="plaintext">.IP</span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="plaintext">* The 'list\-variants[\-zs]' modifier causes variant IDs used for scoring to</span>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="plaintext">.IP</span>
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1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="plaintext">be written to <output prefix>.sscore.vars[.zst].</span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="plaintext">.IP</span>
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1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="plaintext">The main report supports the following column sets:</span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="plaintext">.IP</span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="plaintext">maybefid: FID, if that column was in the input.</span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="plaintext">fid: Force FID column to be written even when absent in the input.</span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="plaintext">(IID is always present, and positioned here.)</span>
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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="plaintext">maybesid: SID, if that column was in the input.</span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="plaintext">sid: Force SID column to be written even when absent in the input.</span>
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1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="plaintext">pheno1: First active phenotype.</span>
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1356
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="plaintext">phenos: All active phenotypes, if any.</span>
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1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="plaintext">nallele: Number of nonmissing alleles.</span>
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1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="plaintext">denom: Denominator of score average (equal to nallele value when</span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="plaintext">.IP</span>
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1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="plaintext">\&'no\-mean\-imputation' specified).</span>
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1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="plaintext">.IP</span>
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1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="plaintext">dosagesum: Sum of named allele dosages.</span>
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1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="plaintext">scoreavgs: Score averages.</span>
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1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="plaintext">scoresums: Score sums.</span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="plaintext">.IP</span>
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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="plaintext">The default is maybefid,maybesid,phenos,nallele,dosagesum,scoreavgs.</span>
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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="plaintext">For more sophisticated polygenic risk scoring, we recommend looking at the</span>
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1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="plaintext">LDpred (https://github.com/bvilhjal/ldpred ) and PRSice\-2</span>
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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="plaintext">(https://www.prsice.info/ ) software packages.</span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="plaintext">.HP</span>
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1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="plaintext">\fB\-\-variant\-score\fR <filename> ['zs'] ['bin' | 'cols='<col set descriptor>]</span>
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1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="plaintext">.IP</span>
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1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="plaintext">(alias: \fB\-\-vscore\fR)</span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="plaintext">Apply linear scoring system(s) to each variant. Each reported variant</span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="plaintext">score is the dot product of a sample\-weight vector with the</span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="plaintext">total\-ALT\-dosage vector, with MAF\-based mean imputation applied to missing</span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="plaintext">dosages.</span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="plaintext">Input file format: one line per sample, each starting with an ID and</span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="plaintext">followed by scoring weight(s); it can also have a header line with the</span>
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1380
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<pre style="margin: 0;">+<span id="LC1380" class="line" lang="plaintext">sample ID representation and the score name(s).</span>
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1381
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<pre style="margin: 0;">+<span id="LC1381" class="line" lang="plaintext">The usual .vscore text report supports the following column sets:</span>
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1382
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="plaintext">.IP</span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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1386
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<pre style="margin: 0;">+<span id="LC1386" class="line" lang="plaintext">ref: Reference allele.</span>
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1387
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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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1389
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="plaintext">altfreq: ALT allele frequency used for mean\-imputation.</span>
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1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="plaintext">nmiss: Number of missing (and thus mean\-imputed) dosages.</span>
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1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="plaintext">nobs: Number of (nonmissing) sample observations.</span>
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1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="plaintext">(Variant scores are always present, and positioned here.)</span>
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1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="plaintext">.IP</span>
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1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="plaintext">Default is chrom,pos,ref,alt.</span>
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1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="plaintext">If binary output is requested instead, the main .vscore.bin matrix contains</span>
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1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="plaintext">double\-precision floating\-point values, column (score) ID(s) are saved to</span>
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1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="plaintext"><output prefix>.vscore.cols, and variant IDs are saved to</span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="plaintext"><output prefix>.vscore.vars[.zst].</span>
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1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="plaintext">.HP</span>
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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="plaintext">\fB\-\-adjust\-file\fR <filename> ['zs'] ['gc'] ['cols='<column set descriptor>]</span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="plaintext">.IP</span>
</pre>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="plaintext">['log10'] ['input\-log10'] ['test='<test name, case\-sensitive>]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="plaintext">.IP</span>
</pre>
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1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="plaintext">Given a file with unfiltered association test results, report some basic</span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="plaintext">multiple\-testing corrections, sorted in increasing\-p\-value order.</span>
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1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="plaintext">* 'gc' causes genomic\-controlled p\-values to be used in the formulas.</span>
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1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="plaintext">.TP</span>
</pre>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="plaintext">(This tends to be overly conservative.</span>
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1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="plaintext">We note that LD Score regression</span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="plaintext">.IP</span>
</pre>
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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="plaintext">usually does a better job of calibrating lambda; see Lee JJ, McGue M,</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="plaintext">Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an</span>
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1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="plaintext">estimator of confounding and genetic correlations in genome\-wide</span>
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1414
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="plaintext">association studies.)</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="plaintext">.IP</span>
</pre>
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1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="plaintext">* 'log10' causes negative base 10 logs of p\-values to be reported, instead</span>
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1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="plaintext">.TP</span>
</pre>
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1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="plaintext">of raw p\-values.</span>
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1419
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<pre style="margin: 0;">+<span id="LC1419" class="line" lang="plaintext">\&'input\-log10' specifies that the input file contains</span>
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1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="plaintext">.HP</span>
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1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="plaintext">\fB\-log10\fR(p) values.</span>
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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="plaintext">.IP</span>
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1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="plaintext">* If the input file contains multiple tests per variant which are</span>
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1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="plaintext">.IP</span>
</pre>
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1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="plaintext">distinguished by a 'TEST' column (true for \fB\-\-linear\fR/\-\-logistic/\-\-glm),</span>
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1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="plaintext">you must use 'test=' to select the test to process.</span>
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1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="plaintext">.IP</span>
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1428
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<pre style="margin: 0;">+<span id="LC1428" class="line" lang="plaintext">The following column sets are supported:</span>
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1429
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<pre style="margin: 0;">+<span id="LC1429" class="line" lang="plaintext">.IP</span>
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1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="plaintext">chrom: Chromosome ID.</span>
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1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="plaintext">pos: Base\-pair coordinate.</span>
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1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="plaintext">(ID is always present, and positioned here.)</span>
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1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="plaintext">ref: Reference allele.</span>
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1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="plaintext">alt1: Alternate allele 1.</span>
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1435
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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="plaintext">alt: All alternate alleles, comma\-separated.</span>
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1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="plaintext">a1: Tested allele. (Omitted if missing from input file.)</span>
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1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="plaintext">unadj: Unadjusted p\-value.</span>
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1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="plaintext">gc: Devlin & Roeder (1999) genomic control corrected p\-value (additive</span>
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1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="plaintext">.IP</span>
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1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="plaintext">models only).</span>
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1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="plaintext">.IP</span>
</pre>
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1442
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<pre style="margin: 0;">+<span id="LC1442" class="line" lang="plaintext">qq: P\-value quantile.</span>
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1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="plaintext">bonf: Bonferroni correction.</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="plaintext">holm: Holm\-Bonferroni (1979) adjusted p\-value.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1445
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="plaintext">sidakss: Sidak single\-step adjusted p\-value.</span>
</pre>
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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="plaintext">sidaksd: Sidak step\-down adjusted p\-value.</span>
</pre>
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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="plaintext">fdrbh: Benjamini & Hochberg (1995) step\-up false discovery control.</span>
</pre>
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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="plaintext">fdrby: Benjamini & Yekutieli (2001) step\-up false discovery control.</span>
</pre>
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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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">Default set is chrom,a1,unadj,gc,bonf,holm,sidakss,sidaksd,fdrbh,fdrby.</span>
</pre>
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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
</td>
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<pre style="margin: 0;">+<span id="LC1451" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-genotyping\-rate\fR ['dosage']</span>
</pre>
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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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="plaintext">Report genotyping rate in log (this was automatic in PLINK 1.x).</span>
</pre>
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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="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-pgen\-info\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">Reports basic information about a .pgen file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-validate\fR</span>
</pre>
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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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">Validates all variant records in a .pgen file.</span>
</pre>
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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
</td>
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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
</td>
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="plaintext">\fB\-\-zst\-decompress\fR <.zst file> [output filename]</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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
</td>
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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1466" class="line" lang="plaintext">(alias: \fB\-\-zd\fR)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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
</td>
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<pre style="margin: 0;">+<span id="LC1467" class="line" lang="plaintext">Decompress a Zstd\-compressed file. If no output filename is specified, the</span>
</pre>
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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="plaintext">file is decompressed to standard output.</span>
</pre>
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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="plaintext">This cannot be used with any other flags, and does not cause a log file to</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">be generated.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">.PP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1472" class="line" lang="plaintext">The following other flags are supported.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1473" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1474" class="line" lang="plaintext">\fB\-\-script\fR <fname></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1475" class="line" lang="plaintext">: Include command\-line options from file.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1476" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1477" class="line" lang="plaintext">\fB\-\-rerun\fR [log]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1478" class="line" lang="plaintext">: Rerun commands in log (default 'plink2.log').</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1479" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1480" class="line" lang="plaintext">\fB\-\-version\fR</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1481" class="line" lang="plaintext">: Display only version number before exiting.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1482" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1483" class="line" lang="plaintext">\fB\-\-silent\fR</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1484" class="line" lang="plaintext">: Suppress regular output to console. (Error\-output is</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1485" class="line" lang="plaintext">not suppressed.)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1486" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1487" class="line" lang="plaintext">\fB\-\-double\-id\fR</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1488" class="line" lang="plaintext">: Set both FIDs and IIDs to the VCF/.bgen sample ID.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1489" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1490" class="line" lang="plaintext">\fB\-\-const\-fid\fR [ID]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1491" class="line" lang="plaintext">: Set all FIDs to the given constant. If '0' (the</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1492" class="line" lang="plaintext">default), no FID column is created.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1493" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1494
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1494" class="line" lang="plaintext">\fB\-\-id\-delim\fR [d]</span>
</pre>
</td>
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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="plaintext">: Normally parses single\-delimiter sample IDs as</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext"><FID><d><IID>, and double\-delimiter IDs as</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext"><FID><d><IID><d><SID>; default delimiter is '_'.</span>
</pre>
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</td>
<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="plaintext">\fB\-\-id\-delim\fR can no longer be used with</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-double\-id\fR/\-\-const\-fid; it will error out if any ID</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">lacks the delimiter.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1502
</td>
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<pre style="margin: 0;">+<span id="LC1502" class="line" lang="plaintext">\fB\-\-idspace\-to\fR <c></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="plaintext">: Convert spaces in VCF/.bgen sample IDs to the given</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1504" class="line" lang="plaintext">character.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1505" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="plaintext">\fB\-\-iid\-sid\fR</span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="plaintext">: Make \fB\-\-id\-delim\fR and \fB\-\-sample\-diff\fR interpret two\-token</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">sample IDs as IID\-SID instead of FID\-IID.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1509" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1510
</td>
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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="plaintext">\fB\-\-vcf\-require\-gt\fR</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">: Skip variants with no GT field.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="plaintext">\fB\-\-vcf\-min\-gq\fR <val></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">: No\-call genotypes when GQ is present and below the</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">threshold.</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="plaintext">\fB\-\-vcf\-max\-dp\fR <val></span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">: No\-call genotypes when DP is present and above/below</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">.TP</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-vcf\-min\-dp\fR <val></span>
</pre>
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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="plaintext">the threshold.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-vcf\-half\-call\fR <m> : Specify how '0/.' and similar VCF GT values should be</span>
</pre>
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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="plaintext">handled. The following four modes are supported:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="plaintext">* 'error'/'e' (default) errors out and reports line #.</span>
</pre>
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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="plaintext">* 'haploid'/'h' treats them as haploid calls.</span>
</pre>
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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="plaintext">* 'missing'/'m' treats them as missing.</span>
</pre>
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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="plaintext">* 'reference'/'r' treats the missing value as 0.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="plaintext">\fB\-\-oxford\-single\-chr\fR <chr name></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">: Specify single\-chromosome .gen/.bgen file</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">with no useful chromosome info inside.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-missing\-code\fR [string list]</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">: Comma\-delimited list of missing phenotype</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="plaintext">(alias: \fB\-\-missing_code\fR)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="plaintext">values for Oxford\-format import (default</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1539
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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="plaintext">\&'NA').</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1541
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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="plaintext">\fB\-\-hard\-call\-threshold\fR <val></span>
</pre>
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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="plaintext">: When importing dosage data, a hardcall is</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1543
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<pre style="margin: 0;">+<span id="LC1543" class="line" lang="plaintext">normally saved when the distance from the</span>
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<td class="diff-line-num new new_line" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1544
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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="plaintext">nearest hardcall, defined as</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1545
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1546
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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="plaintext">0.5 * sum_i |x_i \- round(x_i)|</span>
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1547
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<pre style="margin: 0;">+<span id="LC1547" class="line" lang="plaintext">(where the x_i's are 0..2 allele dosages),</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="plaintext">is not greater than 0.1. You can adjust</span>
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<td class="diff-line-num new new_line" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1549
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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="plaintext">this threshold by providing a numeric</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="plaintext">argument to \fB\-\-hard\-call\-threshold\fR.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1551
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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="plaintext">You can also use this with \fB\-\-make\-[b]pgen\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1552
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<pre style="margin: 0;">+<span id="LC1552" class="line" lang="plaintext">to alter the saved hardcalls while leaving</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="plaintext">the dosages untouched, or \fB\-\-make\-bed\fR to</span>
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1554
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<pre style="margin: 0;">+<span id="LC1554" class="line" lang="plaintext">tweak hardcall export.</span>
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<td class="diff-line-num new new_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1555
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<pre style="margin: 0;">+<span id="LC1555" class="line" lang="plaintext">.TP</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="plaintext">\fB\-\-dosage\-erase\-threshold\fR <val></span>
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1557
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<pre style="margin: 0;">+<span id="LC1557" class="line" lang="plaintext">: \fB\-\-hard\-call\-threshold\fR normally preserves</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="plaintext">the original dosages, and several PLINK 2</span>
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1559
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<pre style="margin: 0;">+<span id="LC1559" class="line" lang="plaintext">commands use them when they're available.</span>
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<td class="diff-line-num new new_line" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1560
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<pre style="margin: 0;">+<span id="LC1560" class="line" lang="plaintext">Use \fB\-\-dosage\-erase\-threshold\fR to make PLINK</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="plaintext">2 erase dosages and keep only hardcalls</span>
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1562
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<pre style="margin: 0;">+<span id="LC1562" class="line" lang="plaintext">when distance\-from\-hardcall <= the given</span>
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1563
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<pre style="margin: 0;">+<span id="LC1563" class="line" lang="plaintext">level.</span>
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<td class="diff-line-num new new_line" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="plaintext">.TP</span>
</pre>
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1565
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="plaintext">\fB\-\-import\-dosage\-certainty\fR <val> : The PLINK 2 file format currently supports</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1566
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<pre style="margin: 0;">+<span id="LC1566" class="line" lang="plaintext">a single dosage for each allele. Some</span>
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1567
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<pre style="margin: 0;">+<span id="LC1567" class="line" lang="plaintext">other dosage file formats include a</span>
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1568
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<pre style="margin: 0;">+<span id="LC1568" class="line" lang="plaintext">separate probability for every possible</span>
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1569
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<pre style="margin: 0;">+<span id="LC1569" class="line" lang="plaintext">genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52,</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="plaintext">P(1/1)=0.28}, a highly uncertain call that</span>
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1571
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="plaintext">is nevertheless treated as a hardcall under</span>
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1572
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="plaintext">\&'\-\-hard\-call\-threshold 0.1'. To make PLINK</span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="plaintext">2 treat a dosage as missing whenever the</span>
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1574
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="plaintext">largest probability is less than a</span>
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1575
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="plaintext">threshold, use \fB\-\-import\-dosage\-certainty\fR.</span>
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1576
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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="plaintext">.TP</span>
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1577
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<pre style="margin: 0;">+<span id="LC1577" class="line" lang="plaintext">\fB\-\-input\-missing\-genotype\fR <c> : '.' is always interpreted as a missing</span>
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1578
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<pre style="margin: 0;">+<span id="LC1578" class="line" lang="plaintext">genotype code in input files. By default, '0'</span>
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1579
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<pre style="margin: 0;">+<span id="LC1579" class="line" lang="plaintext">also is; you can change this second missing</span>
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1580
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<pre style="margin: 0;">+<span id="LC1580" class="line" lang="plaintext">code with \fB\-\-input\-missing\-genotype\fR.</span>
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1581
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<pre style="margin: 0;">+<span id="LC1581" class="line" lang="plaintext">.TP</span>
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1582
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<pre style="margin: 0;">+<span id="LC1582" class="line" lang="plaintext">\fB\-\-allow\-extra\-chr\fR</span>
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1583
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<pre style="margin: 0;">+<span id="LC1583" class="line" lang="plaintext">: Permit unrecognized chromosome codes (alias \fB\-\-aec\fR).</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="plaintext">.HP</span>
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1585
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<pre style="margin: 0;">+<span id="LC1585" class="line" lang="plaintext">\fB\-\-chr\-set\fR <autosome ct> ['no\-x'] ['no\-y'] ['no\-xy'] ['no\-mt'] :</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="plaintext">.TP</span>
</pre>
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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="plaintext">Specify a nonhuman chromosome set.</span>
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1588
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<pre style="margin: 0;">+<span id="LC1588" class="line" lang="plaintext">The first parameter sets the number of</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="plaintext">.IP</span>
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1590
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<pre style="margin: 0;">+<span id="LC1590" class="line" lang="plaintext">diploid autosome pairs if positive, or haploid chromosomes if negative.</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="plaintext">Given diploid autosomes, the remaining modifiers indicate the absence of</span>
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1592
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<pre style="margin: 0;">+<span id="LC1592" class="line" lang="plaintext">the named non\-autosomal chromosomes.</span>
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1593
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<pre style="margin: 0;">+<span id="LC1593" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1594
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<pre style="margin: 0;">+<span id="LC1594" class="line" lang="plaintext">\fB\-\-cow\fR/\-\-dog/\-\-horse/\-\-mouse/\-\-rice/\-\-sheep : Shortcuts for those species.</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="plaintext">.TP</span>
</pre>
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1596
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<pre style="margin: 0;">+<span id="LC1596" class="line" lang="plaintext">\fB\-\-autosome\-num\fR <val></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="plaintext">: Alias for '\-\-chr\-set <value> no\-y no\-xy no\-mt'.</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="plaintext">.TP</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="plaintext">\fB\-\-human\fR</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="plaintext">: Explicitly specify human chromosome set, and make</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="plaintext">output .pvar/VCF files include a ##chrSet header</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="plaintext">line. (.pvar/VCF output files automatically</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="plaintext">include ##chrSet when a nonhuman set is specified.)</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-chr\-override\fR ['file'] : By default, if \fB\-\-chr\-set\fR/\-\-autosome\-num/\-\-cow/etc.</span>
</pre>
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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="plaintext">conflicts with an input file ##chrSet header line,</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="plaintext">PLINK 2 will error out. \fB\-\-chr\-override\fR with no</span>
</pre>
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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="plaintext">argument causes the command line to take</span>
</pre>
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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="plaintext">precedence; '\-\-chr\-override file' defers to the</span>
</pre>
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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="plaintext">file.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-var\-min\-qual\fR <val></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">: Skip variants with low/missing QUAL.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-var\-filter\fR [exception(s)...]</span>
</pre>
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</td>
<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="plaintext">: Skip variants which have FILTER failures.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.HP</span>
</pre>
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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="plaintext">\fB\-\-extract\-if\-info\fR <key> <op> <val> : Exclude variants which don't/do satisfy</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-exclude\-if\-info\fR <key> <op> <val></span>
</pre>
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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="plaintext">a comparison predicate on an INFO key,</span>
</pre>
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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="plaintext">.TP</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="plaintext">(aliases: \fB\-\-extract\-if\fR,</span>
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1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="plaintext">e.g.</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="plaintext">.TP</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="plaintext">\fB\-\-exclude\-if\fR)</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="plaintext">\fB\-\-extract\-if\-info\fR "VT == SNP"</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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1629
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="plaintext">Unless the operator is !=, the predicate</span>
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1630
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="plaintext">always evaluates to false when the key</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="plaintext">is missing.</span>
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<td class="diff-line-num new new_line" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1632
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<pre style="margin: 0;">+<span id="LC1632" class="line" lang="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-require\-info\fR <key(s)...></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="plaintext">: Exclude variants based on nonexistence</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="plaintext">.TP</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="plaintext">\fB\-\-require\-no\-info\fR <key(s)...></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="plaintext">or existence of an INFO key. "<key>=."</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="plaintext">is treated as nonexistence.</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="plaintext">.HP</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="plaintext">\fB\-\-extract\-col\-cond\fR <f> [valcol] [IDcol] [skip] :</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="plaintext">.HP</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="plaintext">\fB\-\-extract\-col\-cond\-match\fR <(sub)string(s)...></span>
</pre>
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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="plaintext">.HP</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="plaintext">\fB\-\-extract\-col\-cond\-mismatch\fR <(sub)string(s)...></span>
</pre>
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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="plaintext">.HP</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="plaintext">\fB\-\-extract\-col\-cond\-substr\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1647
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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1648
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<pre style="margin: 0;">+<span id="LC1648" class="line" lang="plaintext">\fB\-\-extract\-col\-cond\-min\fR <min></span>
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1649
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<pre style="margin: 0;">+<span id="LC1649" class="line" lang="plaintext">.HP</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="plaintext">\fB\-\-extract\-col\-cond\-max\fR <max> :</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="plaintext">.IP</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="plaintext">Exclude all variants without a value\-column entry satisfying a condition.</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="plaintext">* By default, values are read from column 2 of the file, and variant IDs</span>
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1654
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<pre style="margin: 0;">+<span id="LC1654" class="line" lang="plaintext">.IP</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="plaintext">are read from column 1.</span>
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1656
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<pre style="margin: 0;">+<span id="LC1656" class="line" lang="plaintext">.IP</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="plaintext">* Three types of conditions are supported:</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="plaintext">.IP</span>
</pre>
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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="plaintext">* When \fB\-\-extract\-col\-cond\-match\fR is specified without</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="plaintext">.HP</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="plaintext">\fB\-\-extract\-col\-cond\-substr\fR, the value is checked for equality with the</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="plaintext">.TP</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="plaintext">given strings, and kept iff one of them matches.</span>
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1664
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<pre style="margin: 0;">+<span id="LC1664" class="line" lang="plaintext">Similarly,</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="plaintext">.HP</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="plaintext">\fB\-\-extract\-col\-cond\-mismatch\fR without \fB\-\-extract\-col\-cond\-substr\fR causes</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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1668
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<pre style="margin: 0;">+<span id="LC1668" class="line" lang="plaintext">the variant to be kept iff the value matches none of the given strings.</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="plaintext">.IP</span>
</pre>
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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="plaintext">* When \fB\-\-extract\-col\-cond\-match\fR and/or \fB\-mismatch\fR are specified with</span>
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1671
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<pre style="margin: 0;">+<span id="LC1671" class="line" lang="plaintext">.HP</span>
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1672
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<pre style="margin: 0;">+<span id="LC1672" class="line" lang="plaintext">\fB\-\-extract\-col\-cond\-substr\fR, the variant is kept iff none of the</span>
</pre>
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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="plaintext">.HP</span>
</pre>
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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="plaintext">\fB\-\-extract\-col\-cond\-mismatch\fR substrings are contained in the value, and</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1675
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<pre style="margin: 0;">+<span id="LC1675" class="line" lang="plaintext">.IP</span>
</pre>
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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="plaintext">either \fB\-\-extract\-col\-cond\-match\fR was unspecified or at least one of its</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="plaintext">substrings is contained.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.IP</span>
</pre>
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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="plaintext">* Otherwise, the value is interpreted as a number, and the variant is</span>
</pre>
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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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">kept if the number is in [<min>, <max>] (default min=0, max=DBL_MAX).</span>
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<td class="diff-line-num new new_line" data-linenumber="1682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1682
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<pre style="margin: 0;">+<span id="LC1682" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-pheno\fR ['iid\-only'] <f> : Specify additional phenotype/covariate file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">Comma\-delimited files with a header line are now</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1685
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<pre style="margin: 0;">+<span id="LC1685" class="line" lang="plaintext">permitted.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1687
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<pre style="margin: 0;">+<span id="LC1687" class="line" lang="plaintext">\fB\-\-pheno\-name\fR <name...></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">: Only load the designated phenotype(s) from the</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-pheno\fR (if one was specified) or .psam (if no</span>
</pre>
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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="plaintext">\fB\-\-pheno\fR) file. Separate multiple names with</span>
</pre>
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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="plaintext">spaces or commas, and use dashes to designate</span>
</pre>
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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="plaintext">ranges.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-pheno\-col\-nums\fR <#...></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">: Only load the phenotype(s) in the designated</span>
</pre>
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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="plaintext">column number(s) from the \fB\-\-pheno\fR file.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1697
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<pre style="margin: 0;">+<span id="LC1697" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1698
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<pre style="margin: 0;">+<span id="LC1698" class="line" lang="plaintext">\fB\-\-no\-psam\-pheno\fR</span>
</pre>
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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="plaintext">: Ignore phenotype(s) in .psam/.fam file.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-strict\-sid0\fR</span>
</pre>
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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="plaintext">: By default, if there is no SID column in the .psam/.fam</span>
</pre>
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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="plaintext">(or \fB\-\-update\-ids\fR) file, but there is one in another</span>
</pre>
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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="plaintext">input file (for e.g. \fB\-\-keep\fR/\-\-remove), the latter SID</span>
</pre>
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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="plaintext">column is ignored; sample IDs are considered matching as</span>
</pre>
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</td>
<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="plaintext">long as FID and IID are equal (with missing FID treated</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="plaintext">as '0'). If you also want to require SID = '0' for a</span>
</pre>
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</td>
<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="plaintext">sample ID match in this situation, add \fB\-\-strict\-sid0\fR.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-input\-missing\-phenotype\fR <v> : Set nonzero number to treat as a missing</span>
</pre>
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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="plaintext">pheno/covar in input files (default \fB\-9\fR).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-no\-input\-missing\-phenotype\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">: Don't treat any nonzero number as a missing</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">pheno/covar. ('NA'/'nan' are still treated</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">as missing.)</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-1\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">: Expect case/control phenotypes in input files</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">to be coded as 0 = control, 1 = case, instead</span>
</pre>
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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="plaintext">of the usual 0 = missing, 1 = ctrl, 2 = case.</span>
</pre>
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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="plaintext">(Unlike PLINK 1.x, this does not force all</span>
</pre>
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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="plaintext">phenotypes to be interpreted as case/ctrl.)</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-missing\-catname\fR <str></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1726
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="plaintext">: Set missing\-categorical\-phenotype string</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="plaintext">(case\-sensitive, default 'NONE').</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-covar\fR ['iid\-only'] <f> : Specify additional covariate file.</span>
</pre>
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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="plaintext">Comma\-delimited files with a header line are now</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="plaintext">permitted.</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-covar\-name\fR <name...></span>
</pre>
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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="plaintext">: Only load the designated covariate(s) from the</span>
</pre>
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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="plaintext">\fB\-\-covar\fR (if one was specified), \fB\-\-pheno\fR (if no</span>
</pre>
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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="plaintext">\fB\-\-covar\fR), or .psam (if no \fB\-\-covar\fR or \fB\-\-pheno\fR)</span>
</pre>
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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="plaintext">file.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-covar\-col\-nums\fR <#...></span>
</pre>
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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="plaintext">: Only load the covariate(s) in the designated</span>
</pre>
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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="plaintext">column number(s) from the \fB\-\-covar\fR (if one was</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="plaintext">specified) or \fB\-\-pheno\fR (if no \fB\-\-covar\fR) file.</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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1744
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="plaintext">\fB\-\-within\fR <f> [new pheno name] : Import a PLINK 1.x categorical phenotype.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">(Phenotype name defaults to 'CATPHENO'.)</span>
</pre>
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1746
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<pre style="margin: 0;">+<span id="LC1746" class="line" lang="plaintext">* If any numeric values are present, ALL</span>
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<td class="diff-line-num new new_line" data-linenumber="1747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="plaintext">.TP</span>
</pre>
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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="plaintext">values must be numeric.</span>
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<td class="diff-line-num new new_line" data-linenumber="1749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1749
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="plaintext">In that case, 'C'</span>
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<td class="diff-line-num new new_line" data-linenumber="1750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1750
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">is added in front of all category names.</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="plaintext">* 'NA' is treated as a missing value.</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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1754
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<pre style="margin: 0;">+<span id="LC1754" class="line" lang="plaintext">\fB\-\-mwithin\fR <n></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1755
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<pre style="margin: 0;">+<span id="LC1755" class="line" lang="plaintext">: Load \fB\-\-within\fR categories from column n+2.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1756
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<pre style="margin: 0;">+<span id="LC1756" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1757
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<pre style="margin: 0;">+<span id="LC1757" class="line" lang="plaintext">\fB\-\-family\fR [new pheno name]</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1758
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="plaintext">: Create a categorical phenotype from FID.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1759
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<pre style="margin: 0;">+<span id="LC1759" class="line" lang="plaintext">Restrictions on and handling of numeric</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1760
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="plaintext">values are the same as for \fB\-\-within\fR.</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1761
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<pre style="margin: 0;">+<span id="LC1761" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1762
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<pre style="margin: 0;">+<span id="LC1762" class="line" lang="plaintext">\fB\-\-family\-missing\-catname\fR <nm> : Make \fB\-\-family\fR treat the specified FID as</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1763
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="plaintext">missing.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1764
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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-keep\fR <fname...></span>
</pre>
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</td>
<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="plaintext">: Exclude all samples not named in a file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-remove\fR <fname...></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">: Exclude all samples named in a file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1770
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<pre style="margin: 0;">+<span id="LC1770" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-keep\-fam\fR <fn...></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">: Exclude all families not named in a file.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1773
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<pre style="margin: 0;">+<span id="LC1773" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1774
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<pre style="margin: 0;">+<span id="LC1774" class="line" lang="plaintext">\fB\-\-remove\-fam\fR <f...></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="plaintext">: Exclude all families named in a file.</span>
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<td class="diff-line-num new new_line" data-linenumber="1776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1776
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<pre style="margin: 0;">+<span id="LC1776" class="line" lang="plaintext">.HP</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="plaintext">\fB\-\-extract\fR [{bed0 | bed1}] <f...> : Usually excludes all variants (not) named</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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1779
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<pre style="margin: 0;">+<span id="LC1779" class="line" lang="plaintext">\fB\-\-exclude\fR [{bed0 | bed1}] <f...></span>
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<td class="diff-line-num new new_line" data-linenumber="1780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1780
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<pre style="margin: 0;">+<span id="LC1780" class="line" lang="plaintext">in the given file(s). When multiple files</span>
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<td class="diff-line-num new new_line" data-linenumber="1781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1781
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<pre style="margin: 0;">+<span id="LC1781" class="line" lang="plaintext">are named, they are concatenated.</span>
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<td class="diff-line-num new new_line" data-linenumber="1782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1782
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<pre style="margin: 0;">+<span id="LC1782" class="line" lang="plaintext">With the 'bed0' or 'bed1' modifier,</span>
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<td class="diff-line-num new new_line" data-linenumber="1783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1783
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<pre style="margin: 0;">+<span id="LC1783" class="line" lang="plaintext">variants outside/inside the positional</span>
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<td class="diff-line-num new new_line" data-linenumber="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1784
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<pre style="margin: 0;">+<span id="LC1784" class="line" lang="plaintext">ranges in the interval\-BED file(s) are</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="plaintext">excluded instead. 'bed0' tells PLINK 2 to</span>
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<td class="diff-line-num new new_line" data-linenumber="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1786
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<pre style="margin: 0;">+<span id="LC1786" class="line" lang="plaintext">assume the interval bounds follow the UCSC</span>
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<td class="diff-line-num new new_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1787
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<pre style="margin: 0;">+<span id="LC1787" class="line" lang="plaintext">0\-based half\-open convention, while 'bed1'</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="plaintext">(equivalent to PLINK 1.9 'range')</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="plaintext">specifies 1\-based fully\-closed.</span>
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<td class="diff-line-num new new_line" data-linenumber="1790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1790
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<pre style="margin: 0;">+<span id="LC1790" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="1791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1791
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<pre style="margin: 0;">+<span id="LC1791" class="line" lang="plaintext">\fB\-\-extract\-intersect\fR [{bed0 | bed1}] <f...> : Just like \fB\-\-extract\fR, except that</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="plaintext">a variant must be in the</span>
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<td class="diff-line-num new new_line" data-linenumber="1793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1793
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<pre style="margin: 0;">+<span id="LC1793" class="line" lang="plaintext">intersection, rather than just</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="plaintext">the union, of the files to</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="plaintext">remain.</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-bed\-border\-bp\fR <n></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="plaintext">: Stretch BED intervals by the given amount on each</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="plaintext">.TP</span>
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1800
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<pre style="margin: 0;">+<span id="LC1800" class="line" lang="plaintext">\fB\-\-bed\-border\-kb\fR <n></span>
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1801
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<pre style="margin: 0;">+<span id="LC1801" class="line" lang="plaintext">side.</span>
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1802
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<pre style="margin: 0;">+<span id="LC1802" class="line" lang="plaintext">.TP</span>
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1803
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<pre style="margin: 0;">+<span id="LC1803" class="line" lang="plaintext">\fB\-\-keep\-cats\fR <filename></span>
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<td class="diff-line-num new new_line" data-linenumber="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1804
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<pre style="margin: 0;">+<span id="LC1804" class="line" lang="plaintext">: These can be used individually or in combination</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-keep\-cat\-names\fR <nm...></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="plaintext">to define a list of categories to keep; all</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="plaintext">samples not in one of the named categories are</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="plaintext">excluded. Use spaces to separate category names</span>
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1810
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<pre style="margin: 0;">+<span id="LC1810" class="line" lang="plaintext">for \fB\-\-keep\-cat\-names\fR. Use the \fB\-\-missing\-catname\fR</span>
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1811
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<pre style="margin: 0;">+<span id="LC1811" class="line" lang="plaintext">value (default 'NONE') to refer to the group of</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="plaintext">uncategorized samples.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1814
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<pre style="margin: 0;">+<span id="LC1814" class="line" lang="plaintext">\fB\-\-keep\-cat\-pheno\fR <pheno> : If more than one categorical phenotype is loaded,</span>
</pre>
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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="plaintext">or you wish to filter on a categorical covariate,</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="plaintext">\fB\-\-keep\-cat\-pheno\fR must be used to specify which</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="plaintext">phenotype/covariate \fB\-\-keep\-cats\fR and</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="plaintext">\fB\-\-keep\-cat\-names\fR apply to.</span>
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<td class="diff-line-num new new_line" data-linenumber="1819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1819
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<pre style="margin: 0;">+<span id="LC1819" class="line" lang="plaintext">.HP</span>
</pre>
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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="plaintext">\fB\-\-remove\-cats\fR <filename> : Exclude all categories named in the file.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1821
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<pre style="margin: 0;">+<span id="LC1821" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1822
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<pre style="margin: 0;">+<span id="LC1822" class="line" lang="plaintext">\fB\-\-remove\-cat\-names\fR <...> : Exclude named categories.</span>
</pre>
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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="plaintext">.HP</span>
</pre>
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1824
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<pre style="margin: 0;">+<span id="LC1824" class="line" lang="plaintext">\fB\-\-remove\-cat\-pheno\fR <phe> : Specify pheno for \fB\-\-remove\-cats\fR/remove\-cat\-names.</span>
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1825
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<pre style="margin: 0;">+<span id="LC1825" class="line" lang="plaintext">.TP</span>
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1826
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<pre style="margin: 0;">+<span id="LC1826" class="line" lang="plaintext">\fB\-\-split\-cat\-pheno\fR [{omit\-most | omit\-last}] ['covar\-01']</span>
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1827
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<pre style="margin: 0;">+<span id="LC1827" class="line" lang="plaintext">[cat. pheno/covar name(s)...] :</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="plaintext">.IP</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="plaintext">Split n\-category phenotype(s) into n (or n\-1, with 'omit\-most'/'omit\-last')</span>
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1830
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<pre style="margin: 0;">+<span id="LC1830" class="line" lang="plaintext">binary phenotypes, with names of the form <orig. pheno name>=<cat. name>.</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="plaintext">(As a consequence, affected phenotypes and categories are not permitted to</span>
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1832
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<pre style="margin: 0;">+<span id="LC1832" class="line" lang="plaintext">contain the '=' character.)</span>
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1833
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<pre style="margin: 0;">+<span id="LC1833" class="line" lang="plaintext">* This happens after all sample filters.</span>
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1834
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<pre style="margin: 0;">+<span id="LC1834" class="line" lang="plaintext">* If no phenotype or covariate names are provided, all categorical</span>
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1835
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<pre style="margin: 0;">+<span id="LC1835" class="line" lang="plaintext">.IP</span>
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1836
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<pre style="margin: 0;">+<span id="LC1836" class="line" lang="plaintext">phenotypes (but not covariates) are processed.</span>
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1837
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<pre style="margin: 0;">+<span id="LC1837" class="line" lang="plaintext">.TP</span>
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1838
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<pre style="margin: 0;">+<span id="LC1838" class="line" lang="plaintext">* By default, generated covariates are coded as 1=false, 2=true.</span>
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1839
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<pre style="margin: 0;">+<span id="LC1839" class="line" lang="plaintext">To code</span>
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<td class="diff-line-num new new_line" data-linenumber="1840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1840
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<pre style="margin: 0;">+<span id="LC1840" class="line" lang="plaintext">.IP</span>
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1841
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<pre style="margin: 0;">+<span id="LC1841" class="line" lang="plaintext">them as 0=false, 1=true instead, add the 'covar\-01' modifier.</span>
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1842
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<pre style="margin: 0;">+<span id="LC1842" class="line" lang="plaintext">.TP</span>
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1843
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<pre style="margin: 0;">+<span id="LC1843" class="line" lang="plaintext">\fB\-\-loop\-cats\fR <pheno/covar></span>
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1844
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<pre style="margin: 0;">+<span id="LC1844" class="line" lang="plaintext">: Run variant filters and subsequent operations</span>
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1845
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<pre style="margin: 0;">+<span id="LC1845" class="line" lang="plaintext">on just the samples in the first category; then</span>
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1846
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<pre style="margin: 0;">+<span id="LC1846" class="line" lang="plaintext">just the samples in the second category; and so</span>
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1847
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<pre style="margin: 0;">+<span id="LC1847" class="line" lang="plaintext">on, for all categories in the named categorical</span>
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1848
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<pre style="margin: 0;">+<span id="LC1848" class="line" lang="plaintext">phenotype.</span>
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1849
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<pre style="margin: 0;">+<span id="LC1849" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="1850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1850
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<pre style="margin: 0;">+<span id="LC1850" class="line" lang="plaintext">\fB\-\-no\-id\-header\fR ['iid\-only'] : Don't include a header line in .id output</span>
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<td class="diff-line-num new new_line" data-linenumber="1851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1851
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<pre style="margin: 0;">+<span id="LC1851" class="line" lang="plaintext">files. This normally forces two\-column FID/IID</span>
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1852
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<pre style="margin: 0;">+<span id="LC1852" class="line" lang="plaintext">output; add 'iid\-only' to force just</span>
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<td class="diff-line-num new new_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1853
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<pre style="margin: 0;">+<span id="LC1853" class="line" lang="plaintext">single\-column IID.</span>
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<td class="diff-line-num new new_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1854
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<pre style="margin: 0;">+<span id="LC1854" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="1855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1855
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<pre style="margin: 0;">+<span id="LC1855" class="line" lang="plaintext">\fB\-\-variance\-standardize\fR [pheno/covar name(s)...]</span>
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<td class="diff-line-num new new_line" data-linenumber="1856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1856
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<pre style="margin: 0;">+<span id="LC1856" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="1857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1857
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<pre style="margin: 0;">+<span id="LC1857" class="line" lang="plaintext">\fB\-\-covar\-variance\-standardize\fR [covar name(s)...] :</span>
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<td class="diff-line-num new new_line" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1858
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<pre style="margin: 0;">+<span id="LC1858" class="line" lang="plaintext">.IP</span>
</pre>
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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="plaintext">Linearly transform named covariates (and quantitative phenotypes, if</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1860
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<pre style="margin: 0;">+<span id="LC1860" class="line" lang="plaintext">\fB\-\-variance\-standardize\fR) to mean\-zero, variance 1. If no arguments are</span>
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<td class="diff-line-num new new_line" data-linenumber="1861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1861
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<pre style="margin: 0;">+<span id="LC1861" class="line" lang="plaintext">provided, all possible phenotypes/covariates are affected.</span>
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<td class="diff-line-num new new_line" data-linenumber="1862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1862
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<pre style="margin: 0;">+<span id="LC1862" class="line" lang="plaintext">This is frequently necessary to prevent multicollinearity when dealing with</span>
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<td class="diff-line-num new new_line" data-linenumber="1863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1863
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<pre style="margin: 0;">+<span id="LC1863" class="line" lang="plaintext">covariates where abs(mean) is much larger than abs(standard deviation),</span>
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<td class="diff-line-num new new_line" data-linenumber="1864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1864
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<pre style="margin: 0;">+<span id="LC1864" class="line" lang="plaintext">such as year of birth.</span>
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<td class="diff-line-num new new_line" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1865
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<pre style="margin: 0;">+<span id="LC1865" class="line" lang="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-quantile\-normalize\fR [...]</span>
</pre>
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1867
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<pre style="margin: 0;">+<span id="LC1867" class="line" lang="plaintext">: Force named covariates and quantitative</span>
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<td class="diff-line-num new new_line" data-linenumber="1868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1868
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<pre style="margin: 0;">+<span id="LC1868" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1869
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<pre style="margin: 0;">+<span id="LC1869" class="line" lang="plaintext">\fB\-\-pheno\-quantile\-normalize\fR [...]</span>
</pre>
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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="plaintext">phenotypes to a N(0,1) distribution,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1871
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<pre style="margin: 0;">+<span id="LC1871" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1872
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<pre style="margin: 0;">+<span id="LC1872" class="line" lang="plaintext">\fB\-\-covar\-quantile\-normalize\fR [...]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1873
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<pre style="margin: 0;">+<span id="LC1873" class="line" lang="plaintext">preserving only the original rank orders.</span>
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<td class="diff-line-num new new_line" data-linenumber="1874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1874
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<pre style="margin: 0;">+<span id="LC1874" class="line" lang="plaintext">.TP</span>
</pre>
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1875
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<pre style="margin: 0;">+<span id="LC1875" class="line" lang="plaintext">\fB\-\-chr\fR <chr(s)...></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1876
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<pre style="margin: 0;">+<span id="LC1876" class="line" lang="plaintext">: Exclude all variants not on the given chromosome(s).</span>
</pre>
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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="plaintext">Valid choices for humans are 0 (unplaced), 1\-22, X, Y,</span>
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<td class="diff-line-num new new_line" data-linenumber="1878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1878
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<pre style="margin: 0;">+<span id="LC1878" class="line" lang="plaintext">XY, MT, PAR1, and PAR2. Separate multiple chromosomes</span>
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<td class="diff-line-num new new_line" data-linenumber="1879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1879
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<pre style="margin: 0;">+<span id="LC1879" class="line" lang="plaintext">with spaces and/or commas, and use a dash (no adjacent</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="plaintext">spaces permitted) to denote a range, e.g.</span>
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<td class="diff-line-num new new_line" data-linenumber="1881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1881
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<pre style="margin: 0;">+<span id="LC1881" class="line" lang="plaintext">\&'\-\-chr 1\-4, 22, par1, x, par2'.</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-not\-chr\fR <...></span>
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<td class="diff-line-num new new_line" data-linenumber="1884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1884
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<pre style="margin: 0;">+<span id="LC1884" class="line" lang="plaintext">: Reverse of \fB\-\-chr\fR (exclude variants on listed</span>
</pre>
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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="plaintext">chromosomes).</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-autosome\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1888
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<pre style="margin: 0;">+<span id="LC1888" class="line" lang="plaintext">: Exclude all non\-autosomal variants.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-autosome\-par\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1891
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<pre style="margin: 0;">+<span id="LC1891" class="line" lang="plaintext">: Exclude all non\-autosomal variants, except those in a</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1892
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<pre style="margin: 0;">+<span id="LC1892" class="line" lang="plaintext">pseudo\-autosomal region.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-snps\-only\fR ['just\-acgt'] : Exclude non\-SNP variants.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1895
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<pre style="margin: 0;">+<span id="LC1895" class="line" lang="plaintext">By default, SNP = all</span>
</pre>
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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="plaintext">allele codes are single\-character (so</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="plaintext">multiallelic variants with a mix of SNPs and</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="plaintext">non\-SNPs are excluded; split your variants first</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="plaintext">if that's a problem).</span>
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1900
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<pre style="margin: 0;">+<span id="LC1900" class="line" lang="plaintext">The 'just\-acgt' modifier restricts SNP codes to</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="plaintext">{A,C,G,T,a,c,g,t,<missing>}.</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="plaintext">.TP</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="plaintext">\fB\-\-from\fR <var ID></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="plaintext">: Use ID(s) to specify a variant range to load. When used</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="plaintext">.TP</span>
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1906
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<pre style="margin: 0;">+<span id="LC1906" class="line" lang="plaintext">\fB\-\-to\fR</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="plaintext"><var ID> together, both variants must be on the same chromosome.</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="plaintext">(\fB\-\-snps\fR can be used to specify intervals which cross</span>
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1909
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<pre style="margin: 0;">+<span id="LC1909" class="line" lang="plaintext">chromosome boundaries.)</span>
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1910
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<pre style="margin: 0;">+<span id="LC1910" class="line" lang="plaintext">.TP</span>
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1911
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<pre style="margin: 0;">+<span id="LC1911" class="line" lang="plaintext">\fB\-\-snp\fR</span>
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1912
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<pre style="margin: 0;">+<span id="LC1912" class="line" lang="plaintext"><var ID> : Specify a single variant to load.</span>
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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="plaintext">.HP</span>
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1914
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<pre style="margin: 0;">+<span id="LC1914" class="line" lang="plaintext">\fB\-\-exclude\-snp\fR <ID> : Specify a single variant to exclude.</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="plaintext">.TP</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="plaintext">\fB\-\-window\fR</span>
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1917
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<pre style="margin: 0;">+<span id="LC1917" class="line" lang="plaintext"><kbs> : With \fB\-\-snp\fR/\-\-exclude\-snp, loads/excludes all variants</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="plaintext">within half the specified kb distance of the named one.</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="plaintext">.TP</span>
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1920
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<pre style="margin: 0;">+<span id="LC1920" class="line" lang="plaintext">\fB\-\-from\-bp\fR <pos></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="plaintext">: Use base\-pair coordinates to define a variant range to</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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-to\-bp\fR</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="plaintext"><pos> load.</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="plaintext">.TP</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="plaintext">\fB\-\-from\-kb\fR <pos></span>
</pre>
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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="plaintext">* You must use these with \fB\-\-chr\fR, specifying a single</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-to\-kb\fR</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="plaintext"><pos> chromosome.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1932
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<pre style="margin: 0;">+<span id="LC1932" class="line" lang="plaintext">\fB\-\-from\-mb\fR <pos></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1933
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<pre style="margin: 0;">+<span id="LC1933" class="line" lang="plaintext">* Decimals and negative numbers are permitted.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-to\-mb\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1936
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<pre style="margin: 0;">+<span id="LC1936" class="line" lang="plaintext"><pos> * The \fB\-\-to\-bp\fR(/\-kb/\-mb) position is no longer permitted</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1937
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<pre style="margin: 0;">+<span id="LC1937" class="line" lang="plaintext">to be smaller than the \fB\-\-from\-bp\fR position.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1938
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<pre style="margin: 0;">+<span id="LC1938" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1939
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<pre style="margin: 0;">+<span id="LC1939" class="line" lang="plaintext">\fB\-\-snps\fR <var IDs...></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">: Use IDs to specify variant range(s) to load or</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1941
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<pre style="margin: 0;">+<span id="LC1941" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1942
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<pre style="margin: 0;">+<span id="LC1942" class="line" lang="plaintext">\fB\-\-exclude\-snps\fR <...></span>
</pre>
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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="plaintext">exclude. E.g. '\-\-snps rs1111\-rs2222, rs3333, rs4444'.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1944
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<pre style="margin: 0;">+<span id="LC1944" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1945
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<pre style="margin: 0;">+<span id="LC1945" class="line" lang="plaintext">\fB\-\-force\-intersect\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">: PLINK 2 normally errors out when multiple variant</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1947
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<pre style="margin: 0;">+<span id="LC1947" class="line" lang="plaintext">inclusion filters (\fB\-\-extract\fR, \fB\-\-extract\-col\-cond\fR,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1948
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<pre style="margin: 0;">+<span id="LC1948" class="line" lang="plaintext">\fB\-\-extract\-intersect\fR, \fB\-\-from\fR/\-\-to, \fB\-\-from\-bp\fR/\-\-to\-bp,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="1949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1949
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<pre style="margin: 0;">+<span id="LC1949" class="line" lang="plaintext">\fB\-\-snp\fR, \fB\-\-snps\fR) are specified. \fB\-\-force\-intersect\fR</span>
</pre>
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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="plaintext">allows the run to proceed; the set intersection will</span>
</pre>
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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="plaintext">be taken.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-thin\fR <p></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1954" class="line" lang="plaintext">: Randomly remove variants, retaining each with prob. p.</span>
</pre>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1955" class="line" lang="plaintext">.TP</span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1956" class="line" lang="plaintext">\fB\-\-thin\-count\fR <n></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1957" class="line" lang="plaintext">: Randomly remove variants until n of them remain.</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1958" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1959" class="line" lang="plaintext">\fB\-\-bp\-space\fR <bps></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1960" class="line" lang="plaintext">: Remove variants so that each pair is no closer than</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1961" class="line" lang="plaintext">the given bp distance.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1962" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1963" class="line" lang="plaintext">\fB\-\-thin\-indiv\fR <p></span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1964" class="line" lang="plaintext">: Randomly remove samples, retaining with prob. p.</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1965" class="line" lang="plaintext">.HP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1966" class="line" lang="plaintext">\fB\-\-thin\-indiv\-count\fR <n> : Randomly remove samples until n of them remain.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1967" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1968" class="line" lang="plaintext">\fB\-\-keep\-col\-match\fR <f> <val(s)...> : Exclude all samples without a 3rd column</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1969" class="line" lang="plaintext">entry in the given file exactly matching</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1970" class="line" lang="plaintext">one of the given strings. (Separate</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1971" class="line" lang="plaintext">multiple strings with spaces.)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1972" class="line" lang="plaintext">.HP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1973" class="line" lang="plaintext">\fB\-\-keep\-col\-match\-name\fR <col name> : Check column with given name instead.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1974" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1975" class="line" lang="plaintext">\fB\-\-keep\-col\-match\-num\fR <n></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1976" class="line" lang="plaintext">: Check nth column instead.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">.HP</span>
</pre>
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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="plaintext">\fB\-\-geno\fR [val] [{dosage | hh\-missing}]</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="plaintext">.HP</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="plaintext">\fB\-\-mind\fR [val] [{dosage | hh\-missing}] :</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="plaintext">.IP</span>
</pre>
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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="plaintext">Exclude variants (\fB\-\-geno\fR) and/or samples (\fB\-\-mind\fR) with missing call</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="plaintext">frequencies greater than a threshold (default 0.1). (Note that the default</span>
</pre>
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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="plaintext">threshold is only applied if \fB\-\-geno\fR/\-\-mind is invoked without an argument;</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="plaintext">when \fB\-\-geno\fR/\-\-mind is not invoked, no missing call frequency ceiling is</span>
</pre>
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</td>
<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="plaintext">enforced at all. Other inclusion/exclusion default thresholds work the</span>
</pre>
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</td>
<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="plaintext">same way.)</span>
</pre>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1988" class="line" lang="plaintext">By default, when a dosage is present but a hardcall is not, the genotype is</span>
</pre>
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</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1989" class="line" lang="plaintext">treated as missing; add the 'dosage' modifier to treat this case as</span>
</pre>
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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="plaintext">nonmissing. Alternatively, you can use 'hh\-missing' to also treat</span>
</pre>
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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="plaintext">heterozygous haploid calls as missing.</span>
</pre>
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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="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-require\-pheno\fR [name(s)...] : Remove samples missing any of the named</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-require\-covar\fR [name(s)...]</span>
</pre>
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</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1996" class="line" lang="plaintext">phenotype(s)/covariate(s). If no arguments</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1997" class="line" lang="plaintext">are provided, all phenotype(s)/covariate(s)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1998" class="line" lang="plaintext">must be present.</span>
</pre>
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</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1999" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2000" class="line" lang="plaintext">\fB\-\-maf\fR [freq] [mode]</span>
</pre>
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</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2001" class="line" lang="plaintext">: Exclude variants with allele frequency lower than a</span>
</pre>
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</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2002" class="line" lang="plaintext">.TP</span>
</pre>
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2003
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<pre style="margin: 0;">+<span id="LC2003" class="line" lang="plaintext">(alias: \fB\-\-min\-af\fR)</span>
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2004
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<pre style="margin: 0;">+<span id="LC2004" class="line" lang="plaintext">threshold (default 0.01). By default, the nonmajor</span>
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2005
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<pre style="margin: 0;">+<span id="LC2005" class="line" lang="plaintext">allele frequency is used; the other supported modes</span>
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2006
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<pre style="margin: 0;">+<span id="LC2006" class="line" lang="plaintext">are 'nref' (non\-reference), 'alt1', and 'minor'</span>
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2007
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<pre style="margin: 0;">+<span id="LC2007" class="line" lang="plaintext">(least frequent). bcftools freq:mode notation is</span>
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2008
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<pre style="margin: 0;">+<span id="LC2008" class="line" lang="plaintext">permitted.</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="plaintext">.HP</span>
</pre>
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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="plaintext">\fB\-\-max\-maf\fR <freq> [mode] : Exclude variants with MAF greater than the</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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2012
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<pre style="margin: 0;">+<span id="LC2012" class="line" lang="plaintext">(alias: \fB\-\-max\-af\fR)</span>
</pre>
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2013
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<pre style="margin: 0;">+<span id="LC2013" class="line" lang="plaintext">threshold.</span>
</pre>
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2014
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<pre style="margin: 0;">+<span id="LC2014" class="line" lang="plaintext">.TP</span>
</pre>
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2015
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<pre style="margin: 0;">+<span id="LC2015" class="line" lang="plaintext">\fB\-\-mac\fR <ct> [mode]</span>
</pre>
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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="plaintext">: Exclude variants with allele dosage lower than the</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">(alias: \fB\-\-min\-ac\fR)</span>
</pre>
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2019
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<pre style="margin: 0;">+<span id="LC2019" class="line" lang="plaintext">given threshold.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-max\-mac\fR <ct> [mode]</span>
</pre>
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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="plaintext">: Exclude variants with allele dosage greater than</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">(alias: \fB\-\-max\-ac\fR)</span>
</pre>
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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="plaintext">the given threshold.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-maf\-succ\fR</span>
</pre>
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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="plaintext">: Rule of succession allele frequency estimation (used in</span>
</pre>
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2029
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<pre style="margin: 0;">+<span id="LC2029" class="line" lang="plaintext">EIGENSOFT). Given j observations of one allele and k</span>
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2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="plaintext">observations of the other for a biallelic variant, infer</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="plaintext">allele frequencies of (j+1) / (j+k+2) and</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="plaintext">(k+1) / (j+k+2), rather than the default j / (j+k) and</span>
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2033
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<pre style="margin: 0;">+<span id="LC2033" class="line" lang="plaintext">k / (j+k).</span>
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2034
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<pre style="margin: 0;">+<span id="LC2034" class="line" lang="plaintext">Note that this does not affect \fB\-\-freq\fR's output.</span>
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2035
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<pre style="margin: 0;">+<span id="LC2035" class="line" lang="plaintext">.TP</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="plaintext">\fB\-\-min\-alleles\fR <ct> : Exclude variants with fewer than the given # of alleles.</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="plaintext">(When a variant has exactly one ALT allele, and it's</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="plaintext">a missing\-code, it's excluded by "\-\-min\-alleles 2".)</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="plaintext">.HP</span>
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2040
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<pre style="margin: 0;">+<span id="LC2040" class="line" lang="plaintext">\fB\-\-max\-alleles\fR <ct> : Exclude variants with more than the given # of alleles.</span>
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2041
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<pre style="margin: 0;">+<span id="LC2041" class="line" lang="plaintext">.TP</span>
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2042
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<pre style="margin: 0;">+<span id="LC2042" class="line" lang="plaintext">\fB\-\-read\-freq\fR <file> : Load allele frequency estimates from the given \fB\-\-freq\fR or</span>
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2043
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<pre style="margin: 0;">+<span id="LC2043" class="line" lang="plaintext">\fB\-\-geno\-counts\fR (or PLINK 1.9 \fB\-\-freqx\fR) report, instead of</span>
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<td class="diff-line-num new new_line" data-linenumber="2044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2044
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<pre style="margin: 0;">+<span id="LC2044" class="line" lang="plaintext">imputing them from the immediate dataset.</span>
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2045
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<pre style="margin: 0;">+<span id="LC2045" class="line" lang="plaintext">.HP</span>
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2046
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<pre style="margin: 0;">+<span id="LC2046" class="line" lang="plaintext">\fB\-\-hwe\fR <p> ['midp'] ['keep\-fewhet'] :</span>
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<td class="diff-line-num new new_line" data-linenumber="2047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2047
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<pre style="margin: 0;">+<span id="LC2047" class="line" lang="plaintext">.IP</span>
</pre>
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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="plaintext">Exclude variants with Hardy\-Weinberg equilibrium exact test p\-values below</span>
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<td class="diff-line-num new new_line" data-linenumber="2049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2049
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<pre style="margin: 0;">+<span id="LC2049" class="line" lang="plaintext">a threshold.</span>
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2050
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<pre style="margin: 0;">+<span id="LC2050" class="line" lang="plaintext">* By default, only founders are considered.</span>
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2051
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<pre style="margin: 0;">+<span id="LC2051" class="line" lang="plaintext">* chrX p\-values are now computed using Graffelman and Weir's method.</span>
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2052
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<pre style="margin: 0;">+<span id="LC2052" class="line" lang="plaintext">* For variants with k alleles with k>2, k separate 'biallelic' tests are</span>
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2053
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<pre style="margin: 0;">+<span id="LC2053" class="line" lang="plaintext">.IP</span>
</pre>
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2054
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<pre style="margin: 0;">+<span id="LC2054" class="line" lang="plaintext">performed, and the variant is filtered out if any of them fail.</span>
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2055
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<pre style="margin: 0;">+<span id="LC2055" class="line" lang="plaintext">.IP</span>
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2056
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<pre style="margin: 0;">+<span id="LC2056" class="line" lang="plaintext">* With 'keep\-fewhet', variants which fail the test in the too\-few\-hets</span>
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2057
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<pre style="margin: 0;">+<span id="LC2057" class="line" lang="plaintext">.TP</span>
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2058
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<pre style="margin: 0;">+<span id="LC2058" class="line" lang="plaintext">direction are not excluded.</span>
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2059
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<pre style="margin: 0;">+<span id="LC2059" class="line" lang="plaintext">On chrX, this uses the ratio between the</span>
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2060
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<pre style="margin: 0;">+<span id="LC2060" class="line" lang="plaintext">.IP</span>
</pre>
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2061
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<pre style="margin: 0;">+<span id="LC2061" class="line" lang="plaintext">Graffelman/Weir p\-value and the female\-only p\-value.</span>
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2062
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<pre style="margin: 0;">+<span id="LC2062" class="line" lang="plaintext">.IP</span>
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2063
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<pre style="margin: 0;">+<span id="LC2063" class="line" lang="plaintext">* There is currently no special handling of case/control phenotypes.</span>
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2064
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<pre style="margin: 0;">+<span id="LC2064" class="line" lang="plaintext">.TP</span>
</pre>
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2065
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<pre style="margin: 0;">+<span id="LC2065" class="line" lang="plaintext">\fB\-\-mach\-r2\-filter\fR [min] [max] : Exclude variants with MaCH imputation quality</span>
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2066
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<pre style="margin: 0;">+<span id="LC2066" class="line" lang="plaintext">metric less than min or greater than max</span>
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2067
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<pre style="margin: 0;">+<span id="LC2067" class="line" lang="plaintext">(defaults 0.1 and 2.0). (Monomorphic</span>
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2068
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<pre style="margin: 0;">+<span id="LC2068" class="line" lang="plaintext">variants, with r2 = nan, are not excluded.)</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="plaintext">* This is NOT identical to the R2 metric</span>
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<td class="diff-line-num new new_line" data-linenumber="2070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2070
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<pre style="margin: 0;">+<span id="LC2070" class="line" lang="plaintext">.TP</span>
</pre>
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2071
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<pre style="margin: 0;">+<span id="LC2071" class="line" lang="plaintext">reported by Minimac3 0.1.13+; see below.</span>
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2072
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<pre style="margin: 0;">+<span id="LC2072" class="line" lang="plaintext">* If a single argument is provided, it is</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="plaintext">.TP</span>
</pre>
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2074
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<pre style="margin: 0;">+<span id="LC2074" class="line" lang="plaintext">treated as the minimum.</span>
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2075
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<pre style="margin: 0;">+<span id="LC2075" class="line" lang="plaintext">* The metric is not computed on chrX and MT.</span>
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2076
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<pre style="margin: 0;">+<span id="LC2076" class="line" lang="plaintext">.TP</span>
</pre>
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2077
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<pre style="margin: 0;">+<span id="LC2077" class="line" lang="plaintext">\fB\-\-minimac3\-r2\-filter\fR <min> [max] : Compute Minimac3 R2 values from scratch,</span>
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2078
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<pre style="margin: 0;">+<span id="LC2078" class="line" lang="plaintext">and exclude variants with R2 less than min</span>
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2079
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<pre style="margin: 0;">+<span id="LC2079" class="line" lang="plaintext">or (if max is provided) greater than max.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2080
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<pre style="margin: 0;">+<span id="LC2080" class="line" lang="plaintext">* Note that this requires phased\-dosage</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2081
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<pre style="margin: 0;">+<span id="LC2081" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2082
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<pre style="margin: 0;">+<span id="LC2082" class="line" lang="plaintext">data for all samples and variants;</span>
</pre>
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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="plaintext">otherwise this will systematically</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2084" class="line" lang="plaintext">underestimate imputation quality, since</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">unphased hardcalls/dosages are treated</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">as if they were maximally uncertain.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2087
</td>
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<pre style="margin: 0;">+<span id="LC2087" class="line" lang="plaintext">(Use \fB\-\-extract\-if\-info\fR/\-\-exclude\-if\-info</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2088
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2088" class="line" lang="plaintext">to filter on precomputed Minimac3 R2 in</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2089
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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="plaintext">a VCF/.pvar INFO column.)</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="2090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2090
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<pre style="margin: 0;">+<span id="LC2090" class="line" lang="plaintext">.TP</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2091
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<pre style="margin: 0;">+<span id="LC2091" class="line" lang="plaintext">\fB\-\-keep\-females\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2092
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<pre style="margin: 0;">+<span id="LC2092" class="line" lang="plaintext">: Exclude male and unknown\-sex samples.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2093
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2094
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="plaintext">\fB\-\-keep\-males\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2095
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<pre style="margin: 0;">+<span id="LC2095" class="line" lang="plaintext">: Exclude female and unknown\-sex samples.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2096
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<pre style="margin: 0;">+<span id="LC2096" class="line" lang="plaintext">.TP</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2097
</td>
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="plaintext">\fB\-\-keep\-nosex\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2098
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="plaintext">: Exclude all known\-sex samples.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2099
</td>
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<pre style="margin: 0;">+<span id="LC2099" class="line" lang="plaintext">.TP</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2100
</td>
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<pre style="margin: 0;">+<span id="LC2100" class="line" lang="plaintext">\fB\-\-remove\-females\fR</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2101" class="line" lang="plaintext">: Exclude female samples.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC2102" class="line" lang="plaintext">.TP</span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC2103" class="line" lang="plaintext">\fB\-\-remove\-males\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC2104" class="line" lang="plaintext">: Exclude male samples.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-remove\-nosex\fR</span>
</pre>
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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="plaintext">: Exclude unknown\-sex samples.</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-keep\-founders\fR</span>
</pre>
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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="plaintext">: Exclude nonfounder samples.</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="plaintext">.HP</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="plaintext">\fB\-\-keep\-nonfounders\fR : Exclude founder samples.</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="plaintext">.HP</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="plaintext">\fB\-\-keep\-if\fR <pheno/covar> <op> <val> : Exclude samples which don't/do satisfy a</span>
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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="plaintext">.TP</span>
</pre>
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2116
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<pre style="margin: 0;">+<span id="LC2116" class="line" lang="plaintext">\fB\-\-remove\-if\fR <pheno/covar> <op> <v></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="plaintext">comparison predicate, e.g.</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="plaintext">\fB\-\-keep\-if\fR "PHENO1 == case"</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="plaintext">.TP</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="plaintext">Unless the operator is !=, the predicate</span>
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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="plaintext">always evaluates to false when the</span>
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2122
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<pre style="margin: 0;">+<span id="LC2122" class="line" lang="plaintext">phenotype/covariate is missing.</span>
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2123
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<pre style="margin: 0;">+<span id="LC2123" class="line" lang="plaintext">.TP</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="plaintext">\fB\-\-nonfounders\fR</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="plaintext">: Include nonfounders in allele freq/HWE calculations.</span>
</pre>
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2126
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<pre style="margin: 0;">+<span id="LC2126" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-bad\-freqs\fR</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="plaintext">: When PLINK 2 needs decent allele frequencies, it</span>
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2129
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<pre style="margin: 0;">+<span id="LC2129" class="line" lang="plaintext">normally errors out if they aren't provided by</span>
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2130
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<pre style="margin: 0;">+<span id="LC2130" class="line" lang="plaintext">\fB\-\-read\-freq\fR and less than 50 founders are available to</span>
</pre>
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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="plaintext">impute them from. Use \fB\-\-bad\-freqs\fR to force PLINK 2 to</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="plaintext">proceed in this case.</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="plaintext">.TP</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="plaintext">\fB\-\-bad\-ld\fR</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="plaintext">: PLINK 2 normally errors out when it needs to estimate LD</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="plaintext">between variants, but there are less than 50 founders to</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">estimate from. Use \fB\-\-bad\-ld\fR to force PLINK 2 to</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="plaintext">proceed.</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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-export\-allele\fR <file> : With \fB\-\-export\fR A/A\-transpose/AD, count alleles named</span>
</pre>
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</td>
<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="plaintext">in the file, instead of REF alleles.</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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-output\-chr\fR <MT code> : Set chromosome coding scheme in output files by</span>
</pre>
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</td>
<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="plaintext">providing the desired human mitochondrial code.</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="plaintext">Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM',</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">and 'chrMT'; default is now 'MT' (note that this is</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="2147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2147
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<pre style="margin: 0;">+<span id="LC2147" class="line" lang="plaintext">a change from PLINK 1.x, which defaulted to '26').</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2149
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<pre style="margin: 0;">+<span id="LC2149" class="line" lang="plaintext">\fB\-\-output\-missing\-genotype\fR <ch> : Set the code used to represent missing</span>
</pre>
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</td>
<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="plaintext">genotypes in output files (default '.').</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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
</td>
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2152
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<pre style="margin: 0;">+<span id="LC2152" class="line" lang="plaintext">\fB\-\-output\-missing\-phenotype\fR <s> : Set the string used to represent missing</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">phenotypes in output files (default 'NA').</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-sort\-vars\fR [mode]</span>
</pre>
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2156
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<pre style="margin: 0;">+<span id="LC2156" class="line" lang="plaintext">: Sort variants by chromosome, then position, then</span>
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2157
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<pre style="margin: 0;">+<span id="LC2157" class="line" lang="plaintext">ID. The following string orders are supported:</span>
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2158
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<pre style="margin: 0;">+<span id="LC2158" class="line" lang="plaintext">* 'natural'/'n': Natural sort (default).</span>
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2159
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<pre style="margin: 0;">+<span id="LC2159" class="line" lang="plaintext">* 'ascii'/'a': ASCII.</span>
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2160
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<pre style="margin: 0;">+<span id="LC2160" class="line" lang="plaintext">This must be used with \fB\-\-make\-[b]pgen\fR/\-\-make\-bed.</span>
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2161
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<pre style="margin: 0;">+<span id="LC2161" class="line" lang="plaintext">.TP</span>
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2162
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<pre style="margin: 0;">+<span id="LC2162" class="line" lang="plaintext">\fB\-\-set\-hh\-missing\fR ['keep\-dosage'] : Make \fB\-\-make\-[b]pgen\fR/\-\-make\-bed set non\-MT</span>
</pre>
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2163
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<pre style="margin: 0;">+<span id="LC2163" class="line" lang="plaintext">heterozygous haploid hardcalls, and all</span>
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2164
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<pre style="margin: 0;">+<span id="LC2164" class="line" lang="plaintext">female chrY calls, to missing. (Unlike</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="plaintext">PLINK 1.x, this treats unknown\-sex chrY</span>
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2166
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<pre style="margin: 0;">+<span id="LC2166" class="line" lang="plaintext">genotypes like males, not females.)</span>
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2167
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<pre style="margin: 0;">+<span id="LC2167" class="line" lang="plaintext">By default, all associated dosages are</span>
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2168
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<pre style="margin: 0;">+<span id="LC2168" class="line" lang="plaintext">also erased; use 'keep\-dosage' to keep</span>
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2169
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<pre style="margin: 0;">+<span id="LC2169" class="line" lang="plaintext">them all.</span>
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2170
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<pre style="margin: 0;">+<span id="LC2170" class="line" lang="plaintext">.TP</span>
</pre>
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2171
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<pre style="margin: 0;">+<span id="LC2171" class="line" lang="plaintext">\fB\-\-set\-mixed\-mt\-missing\fR ['keep\-dosage'] : Make \fB\-\-make\-[b]pgen\fR/\-\-make\-bed set</span>
</pre>
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2172
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<pre style="margin: 0;">+<span id="LC2172" class="line" lang="plaintext">mixed MT hardcalls to missing.</span>
</pre>
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2173
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<pre style="margin: 0;">+<span id="LC2173" class="line" lang="plaintext">.HP</span>
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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="plaintext">\fB\-\-split\-par\fR <bp1> <bp2> : Changes chromosome code of all X chromosome</span>
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2175
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<pre style="margin: 0;">+<span id="LC2175" class="line" lang="plaintext">.TP</span>
</pre>
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2176
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<pre style="margin: 0;">+<span id="LC2176" class="line" lang="plaintext">\fB\-\-split\-par\fR <build></span>
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2177
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<pre style="margin: 0;">+<span id="LC2177" class="line" lang="plaintext">variants with bp position <= bp1 to PAR1, and those</span>
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2178
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<pre style="margin: 0;">+<span id="LC2178" class="line" lang="plaintext">with position >= bp2 to PAR2. The following build</span>
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2179
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<pre style="margin: 0;">+<span id="LC2179" class="line" lang="plaintext">codes are supported as shorthand:</span>
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2180
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<pre style="margin: 0;">+<span id="LC2180" class="line" lang="plaintext">* 'b36'/'hg18' = NCBI 36, 2709521/154584237</span>
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2181
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<pre style="margin: 0;">+<span id="LC2181" class="line" lang="plaintext">* 'b37'/'hg19' = GRCh37, 2699520/154931044</span>
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2182
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<pre style="margin: 0;">+<span id="LC2182" class="line" lang="plaintext">* 'b38'/'hg38' = GRCh38, 2781479/155701383</span>
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2183
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<pre style="margin: 0;">+<span id="LC2183" class="line" lang="plaintext">.TP</span>
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2184
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<pre style="margin: 0;">+<span id="LC2184" class="line" lang="plaintext">\fB\-\-merge\-par\fR</span>
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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="plaintext">: Merge PAR1/PAR2 back with X. Requires PAR1 to be</span>
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2186
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<pre style="margin: 0;">+<span id="LC2186" class="line" lang="plaintext">positioned immediately before X, and PAR2 to be</span>
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2187
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<pre style="margin: 0;">+<span id="LC2187" class="line" lang="plaintext">immediately after X. (Should *not* be used with</span>
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2188
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<pre style="margin: 0;">+<span id="LC2188" class="line" lang="plaintext">"\-\-export vcf", since it causes male</span>
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2189
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<pre style="margin: 0;">+<span id="LC2189" class="line" lang="plaintext">homozygous/missing calls in PAR1/PAR2 to be</span>
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2190
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<pre style="margin: 0;">+<span id="LC2190" class="line" lang="plaintext">reported as haploid.)</span>
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2191
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<pre style="margin: 0;">+<span id="LC2191" class="line" lang="plaintext">.TP</span>
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2192
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<pre style="margin: 0;">+<span id="LC2192" class="line" lang="plaintext">\fB\-\-merge\-x\fR</span>
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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="plaintext">: Merge XY back with X. This usually has to be</span>
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2194
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<pre style="margin: 0;">+<span id="LC2194" class="line" lang="plaintext">combined with \fB\-\-sort\-vars\fR.</span>
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2195
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<pre style="margin: 0;">+<span id="LC2195" class="line" lang="plaintext">.TP</span>
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2196
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<pre style="margin: 0;">+<span id="LC2196" class="line" lang="plaintext">\fB\-\-set\-missing\-var\-ids\fR <t></span>
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2197
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<pre style="margin: 0;">+<span id="LC2197" class="line" lang="plaintext">: Given a template string with a '@' where the</span>
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2198
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<pre style="margin: 0;">+<span id="LC2198" class="line" lang="plaintext">.TP</span>
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2199
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<pre style="margin: 0;">+<span id="LC2199" class="line" lang="plaintext">\fB\-\-set\-all\-var\-ids\fR <t></span>
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2200
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<pre style="margin: 0;">+<span id="LC2200" class="line" lang="plaintext">chromosome code should go and '#' where the bp</span>
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2201
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<pre style="margin: 0;">+<span id="LC2201" class="line" lang="plaintext">coordinate belongs, \fB\-\-set\-missing\-var\-ids\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="2202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2202
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<pre style="margin: 0;">+<span id="LC2202" class="line" lang="plaintext">assigns chromosome\-and\-bp\-based IDs to unnamed</span>
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<td class="diff-line-num new new_line" data-linenumber="2203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2203
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<pre style="margin: 0;">+<span id="LC2203" class="line" lang="plaintext">variants, while \fB\-\-set\-all\-var\-ids\fR resets all</span>
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2204
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<pre style="margin: 0;">+<span id="LC2204" class="line" lang="plaintext">IDs.</span>
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2205
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<pre style="margin: 0;">+<span id="LC2205" class="line" lang="plaintext">You may also use '$r'/'$a' to refer to the</span>
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2206
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<pre style="margin: 0;">+<span id="LC2206" class="line" lang="plaintext">ref and alt1 alleles, or '$1'/'$2' to refer to</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2207
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<pre style="margin: 0;">+<span id="LC2207" class="line" lang="plaintext">them in alphabetical order.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2208
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<pre style="margin: 0;">+<span id="LC2208" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2209
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<pre style="margin: 0;">+<span id="LC2209" class="line" lang="plaintext">\fB\-\-var\-id\-multi\fR <t></span>
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<td class="diff-line-num new new_line" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2210
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<pre style="margin: 0;">+<span id="LC2210" class="line" lang="plaintext">: Specify alternative templates for multiallelic</span>
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<td class="diff-line-num new new_line" data-linenumber="2211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2211
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<pre style="margin: 0;">+<span id="LC2211" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2212
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<pre style="margin: 0;">+<span id="LC2212" class="line" lang="plaintext">\fB\-\-var\-id\-multi\-nonsnp\fR <t></span>
</pre>
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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="plaintext">variants. ('$a' and '$1'/'$2' should be avoided</span>
</pre>
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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="plaintext">here, though they're technically still allowed.)</span>
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<td class="diff-line-num new new_line" data-linenumber="2215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2215
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<pre style="margin: 0;">+<span id="LC2215" class="line" lang="plaintext">.HP</span>
</pre>
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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="plaintext">\fB\-\-new\-id\-max\-allele\-len\fR <len> [{error | missing | truncate}] :</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2217
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<pre style="margin: 0;">+<span id="LC2217" class="line" lang="plaintext">.IP</span>
</pre>
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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="plaintext">Specify maximum number of leading characters from allele codes to include</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2219
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<pre style="margin: 0;">+<span id="LC2219" class="line" lang="plaintext">in new variant IDs, and behavior on longer codes (defaults 23, error).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2220
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<pre style="margin: 0;">+<span id="LC2220" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2221
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<pre style="margin: 0;">+<span id="LC2221" class="line" lang="plaintext">\fB\-\-missing\-var\-code\fR <str></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2222
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<pre style="margin: 0;">+<span id="LC2222" class="line" lang="plaintext">: Change unnamed variant code for \fB\-\-rm\-dup\fR,</span>
</pre>
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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="plaintext">\fB\-\-set\-\fR{missing|all}\-var\-ids, and</span>
</pre>
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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="plaintext">\fB\-\-recover\-var\-ids\fR (default '.').</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-update\-map\fR</span>
</pre>
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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="plaintext"><f> [bpcol] [IDcol] [skip] : Update variant bp positions.</span>
</pre>
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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="plaintext">.HP</span>
</pre>
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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="plaintext">\fB\-\-update\-name\fR <f> [newcol] [oldcol] [skip] : Update variant IDs.</span>
</pre>
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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="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2231
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<pre style="margin: 0;">+<span id="LC2231" class="line" lang="plaintext">\fB\-\-recover\-var\-ids\fR <file> ['strict\-bim\-order'] [{rigid | force}] ['partial'] :</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="plaintext">.TP</span>
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2233
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<pre style="margin: 0;">+<span id="LC2233" class="line" lang="plaintext">Undo \fB\-\-set\-all\-var\-ids\fR, given the original .pvar/VCF/.bim file.</span>
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2234
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<pre style="margin: 0;">+<span id="LC2234" class="line" lang="plaintext">Original</span>
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2235
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<pre style="margin: 0;">+<span id="LC2235" class="line" lang="plaintext">.IP</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="plaintext">IDs are looked up by position and allele codes.</span>
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2237
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<pre style="margin: 0;">+<span id="LC2237" class="line" lang="plaintext">* By default, if the original\-ID file is a .bim, allele order is ignored.</span>
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2238
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<pre style="margin: 0;">+<span id="LC2238" class="line" lang="plaintext">.IP</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="plaintext">Use 'strict\-bim\-order' to force A1=ALT, A2=REF.</span>
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2240
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<pre style="margin: 0;">+<span id="LC2240" class="line" lang="plaintext">.IP</span>
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2241
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<pre style="margin: 0;">+<span id="LC2241" class="line" lang="plaintext">* If any variant has multiple matching records in the original\-ID file, and</span>
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2242
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<pre style="margin: 0;">+<span id="LC2242" class="line" lang="plaintext">.IP</span>
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2243
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<pre style="margin: 0;">+<span id="LC2243" class="line" lang="plaintext">the IDs conflict, \fB\-\-recover\-var\-ids\fR writes the affected (current) ID(s)</span>
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2244
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<pre style="margin: 0;">+<span id="LC2244" class="line" lang="plaintext">to <output prefix>.recoverid.dup, and normally errors out. If the</span>
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2245
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<pre style="margin: 0;">+<span id="LC2245" class="line" lang="plaintext">original\-ID file has the same number of variants in the same order, you</span>
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2246
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<pre style="margin: 0;">+<span id="LC2246" class="line" lang="plaintext">can still recover the old IDs with the 'rigid' modifier in this case.</span>
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2247
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<pre style="margin: 0;">+<span id="LC2247" class="line" lang="plaintext">Alternatively, to proceed and assign the missing\-ID code to these</span>
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2248
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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="plaintext">variants, add the 'force' modifier. (The .recoverid.dup file is still</span>
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2249
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<pre style="margin: 0;">+<span id="LC2249" class="line" lang="plaintext">written when 'rigid' or 'force' is specified.)</span>
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<td class="diff-line-num new new_line" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2250
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<pre style="margin: 0;">+<span id="LC2250" class="line" lang="plaintext">.IP</span>
</pre>
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2251
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<pre style="margin: 0;">+<span id="LC2251" class="line" lang="plaintext">* \fB\-\-recover\-var\-ids\fR normally expects to replace all variant IDs, and errors</span>
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2252
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<pre style="margin: 0;">+<span id="LC2252" class="line" lang="plaintext">.TP</span>
</pre>
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2253
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<pre style="margin: 0;">+<span id="LC2253" class="line" lang="plaintext">out if any are left untouched.</span>
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2254
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<pre style="margin: 0;">+<span id="LC2254" class="line" lang="plaintext">Add the 'partial' modifier when you</span>
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2255
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<pre style="margin: 0;">+<span id="LC2255" class="line" lang="plaintext">.IP</span>
</pre>
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2256
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<pre style="margin: 0;">+<span id="LC2256" class="line" lang="plaintext">actually want to update just a proper subset.</span>
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2257
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<pre style="margin: 0;">+<span id="LC2257" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2258
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<pre style="margin: 0;">+<span id="LC2258" class="line" lang="plaintext">\fB\-\-update\-alleles\fR <fname></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2259
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<pre style="margin: 0;">+<span id="LC2259" class="line" lang="plaintext">: Update variant allele codes.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-update\-ids\fR <fname></span>
</pre>
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</td>
<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="plaintext">: Update sample IDs.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2264
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<pre style="margin: 0;">+<span id="LC2264" class="line" lang="plaintext">\fB\-\-update\-parents\fR <fname></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2265
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<pre style="margin: 0;">+<span id="LC2265" class="line" lang="plaintext">: Update parental IDs.</span>
</pre>
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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="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2267
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<pre style="margin: 0;">+<span id="LC2267" class="line" lang="plaintext">\fB\-\-update\-sex\fR <filename> ['col\-num='<n>] ['male0'] :</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2268
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<pre style="margin: 0;">+<span id="LC2268" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2269
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<pre style="margin: 0;">+<span id="LC2269" class="line" lang="plaintext">Update sex information.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2270
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<pre style="margin: 0;">+<span id="LC2270" class="line" lang="plaintext">* By default, if there is a header line starting with '#FID'/'#IID', sex is</span>
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<td class="diff-line-num new new_line" data-linenumber="2271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2271
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<pre style="margin: 0;">+<span id="LC2271" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2272
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<pre style="margin: 0;">+<span id="LC2272" class="line" lang="plaintext">loaded from the first column titled 'SEX' (any capitalization);</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2273
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<pre style="margin: 0;">+<span id="LC2273" class="line" lang="plaintext">otherwise, column 3 is assumed. Use 'col\-num=' to force a column number.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2274
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<pre style="margin: 0;">+<span id="LC2274" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2275
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<pre style="margin: 0;">+<span id="LC2275" class="line" lang="plaintext">* Only the first character in the sex column is processed.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2276
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<pre style="margin: 0;">+<span id="LC2276" class="line" lang="plaintext">By default,</span>
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<td class="diff-line-num new new_line" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2277
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<pre style="margin: 0;">+<span id="LC2277" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2278
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<pre style="margin: 0;">+<span id="LC2278" class="line" lang="plaintext">\&'1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2279
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<pre style="margin: 0;">+<span id="LC2279" class="line" lang="plaintext">and '0'/'N' is interpreted as unknown\-sex. To change this to '0'/'M'/'m'</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2280
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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="plaintext">= male, '1'/'F'/'f' = female, anything else other than '2' = unknown\-sex,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2281
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<pre style="margin: 0;">+<span id="LC2281" class="line" lang="plaintext">add 'male0'.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2282
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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="plaintext">.TP</span>
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2283
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<pre style="margin: 0;">+<span id="LC2283" class="line" lang="plaintext">\fB\-\-real\-ref\-alleles\fR</span>
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2284
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<pre style="margin: 0;">+<span id="LC2284" class="line" lang="plaintext">: Treat A2 alleles in a PLINK 1.x fileset as actual REF</span>
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2285
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<pre style="margin: 0;">+<span id="LC2285" class="line" lang="plaintext">alleles; otherwise they're marked as provisional.</span>
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2286
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<pre style="margin: 0;">+<span id="LC2286" class="line" lang="plaintext">.TP</span>
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2287
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<pre style="margin: 0;">+<span id="LC2287" class="line" lang="plaintext">\fB\-\-maj\-ref\fR ['force'] : Set major alleles to reference, like PLINK 1.x</span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="plaintext">automatically did. (Note that this is now opt\-in</span>
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2289
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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="plaintext">rather than opt\-out; \fB\-\-keep\-allele\-order\fR is no longer</span>
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2290
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<pre style="margin: 0;">+<span id="LC2290" class="line" lang="plaintext">necessary to prevent allele\-swapping.)</span>
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2291
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<pre style="margin: 0;">+<span id="LC2291" class="line" lang="plaintext">* This can only be used in runs with</span>
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2292
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="plaintext">.TP</span>
</pre>
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2293
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<pre style="margin: 0;">+<span id="LC2293" class="line" lang="plaintext">\fB\-\-make\-bed\fR/\-\-make\-[b]pgen/\-\-export and no other</span>
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2294
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<pre style="margin: 0;">+<span id="LC2294" class="line" lang="plaintext">commands.</span>
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2295
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<pre style="margin: 0;">+<span id="LC2295" class="line" lang="plaintext">.TP</span>
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2296
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<pre style="margin: 0;">+<span id="LC2296" class="line" lang="plaintext">* By default, this only affects variants marked as</span>
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2297
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<pre style="margin: 0;">+<span id="LC2297" class="line" lang="plaintext">having 'provisional' reference alleles. Add 'force'</span>
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2298
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<pre style="margin: 0;">+<span id="LC2298" class="line" lang="plaintext">to apply this to all variants.</span>
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2299
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<pre style="margin: 0;">+<span id="LC2299" class="line" lang="plaintext">.IP</span>
</pre>
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2300
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<pre style="margin: 0;">+<span id="LC2300" class="line" lang="plaintext">* All new reference alleles are marked as provisional.</span>
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<td class="diff-line-num new new_line" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2301
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<pre style="margin: 0;">+<span id="LC2301" class="line" lang="plaintext">.HP</span>
</pre>
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2302
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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="plaintext">\fB\-\-ref\-allele\fR ['force'] <filename> [refcol] [IDcol] [skip]</span>
</pre>
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2303
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<pre style="margin: 0;">+<span id="LC2303" class="line" lang="plaintext">.HP</span>
</pre>
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2304
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<pre style="margin: 0;">+<span id="LC2304" class="line" lang="plaintext">\fB\-\-alt1\-allele\fR ['force'] <filename> [alt1col] [IDcol] [skip] :</span>
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2305
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<pre style="margin: 0;">+<span id="LC2305" class="line" lang="plaintext">.IP</span>
</pre>
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2306
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<pre style="margin: 0;">+<span id="LC2306" class="line" lang="plaintext">These set the alleles specified in the file to ref (\fB\-\-ref\-allele\fR) or alt1</span>
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2307
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<pre style="margin: 0;">+<span id="LC2307" class="line" lang="plaintext">(\fB\-\-alt1\-allele\fR). They can be combined in the same run.</span>
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2308
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<pre style="margin: 0;">+<span id="LC2308" class="line" lang="plaintext">* These can only be used in runs with \fB\-\-make\-bed\fR/\-\-make\-[b]pgen/\-\-export</span>
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2309
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<pre style="margin: 0;">+<span id="LC2309" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2310
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<pre style="margin: 0;">+<span id="LC2310" class="line" lang="plaintext">and no other commands.</span>
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<td class="diff-line-num new new_line" data-linenumber="2311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2311
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<pre style="margin: 0;">+<span id="LC2311" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2312
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<pre style="margin: 0;">+<span id="LC2312" class="line" lang="plaintext">* "\-\-ref\-allele <VCF filename> 4 3 '#'", which scrapes reference allele</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="plaintext">.IP</span>
</pre>
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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="plaintext">assignments from a VCF file, is especially useful.</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="plaintext">.IP</span>
</pre>
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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="plaintext">* By default, these error out when asked to change a 'known' reference</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="plaintext">.TP</span>
</pre>
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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="plaintext">allele.</span>
</pre>
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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="plaintext">Add 'force' to permit that (when e.g. switching to a new</span>
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<td class="diff-line-num new new_line" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2320
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<pre style="margin: 0;">+<span id="LC2320" class="line" lang="plaintext">.IP</span>
</pre>
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2321
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<pre style="margin: 0;">+<span id="LC2321" class="line" lang="plaintext">reference genome).</span>
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2322
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<pre style="margin: 0;">+<span id="LC2322" class="line" lang="plaintext">.IP</span>
</pre>
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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="plaintext">* When \fB\-\-alt1\-allele\fR changes the previous ref allele to alt1, the previous</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2324
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<pre style="margin: 0;">+<span id="LC2324" class="line" lang="plaintext">.IP</span>
</pre>
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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="plaintext">alt1 allele is set to reference and marked as provisional.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2327
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<pre style="margin: 0;">+<span id="LC2327" class="line" lang="plaintext">\fB\-\-ref\-from\-fa\fR ['force'] : This sets reference alleles from the \fB\-\-fa\fR file when</span>
</pre>
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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="plaintext">it can be done unambiguously (note that it's never</span>
</pre>
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2329
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<pre style="margin: 0;">+<span id="LC2329" class="line" lang="plaintext">possible for deletions or some insertions).</span>
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<td class="diff-line-num new new_line" data-linenumber="2330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2330
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<pre style="margin: 0;">+<span id="LC2330" class="line" lang="plaintext">By default, it errors out when asked to change a</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2331
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<pre style="margin: 0;">+<span id="LC2331" class="line" lang="plaintext">\&'known' reference allele; add the 'force' modifier</span>
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<td class="diff-line-num new new_line" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2332
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<pre style="margin: 0;">+<span id="LC2332" class="line" lang="plaintext">to permit that.</span>
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2333
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<pre style="margin: 0;">+<span id="LC2333" class="line" lang="plaintext">.TP</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="plaintext">\fB\-\-normalize\fR ['list']</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="plaintext">: Left\-normalize all variants, using the \fB\-\-fa\fR file.</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="plaintext">.TP</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="plaintext">(alias: \fB\-\-norm\fR)</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="plaintext">(Assumes no differences in capitalization.) The</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="plaintext">\&'list' modifier causes a list of affected variant</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="plaintext">IDs to be written to <output prefix>.normalized.</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="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="2342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2342
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<pre style="margin: 0;">+<span id="LC2342" class="line" lang="plaintext">\fB\-\-indiv\-sort\fR <mode> [f] : Specify sample ID sort order for merge and</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="plaintext">\fB\-\-make\-[b]pgen\fR/\-\-make\-bed. The following four</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="plaintext">modes are supported:</span>
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2345
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<pre style="margin: 0;">+<span id="LC2345" class="line" lang="plaintext">* 'none'/'0' keeps samples in the order they were</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="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="2347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2347
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<pre style="margin: 0;">+<span id="LC2347" class="line" lang="plaintext">loaded.</span>
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<td class="diff-line-num new new_line" data-linenumber="2348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2348
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<pre style="margin: 0;">+<span id="LC2348" class="line" lang="plaintext">Default for non\-merge.</span>
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<td class="diff-line-num new new_line" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2349
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<pre style="margin: 0;">+<span id="LC2349" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2350
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<pre style="margin: 0;">+<span id="LC2350" class="line" lang="plaintext">* 'natural'/'n' invokes "natural sort", e.g.</span>
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<td class="diff-line-num new new_line" data-linenumber="2351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2351
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<pre style="margin: 0;">+<span id="LC2351" class="line" lang="plaintext">\&'id2' < 'ID3' < 'id10'. Default when merging.</span>
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<td class="diff-line-num new new_line" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2352
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<pre style="margin: 0;">+<span id="LC2352" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2353
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<pre style="margin: 0;">+<span id="LC2353" class="line" lang="plaintext">* 'ascii'/'a' sorts in ASCII order, e.g.</span>
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2354
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<pre style="margin: 0;">+<span id="LC2354" class="line" lang="plaintext">\&'ID3' < 'id10' < 'id2'.</span>
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<td class="diff-line-num new new_line" data-linenumber="2355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2355
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<pre style="margin: 0;">+<span id="LC2355" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2356
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<pre style="margin: 0;">+<span id="LC2356" class="line" lang="plaintext">* 'file'/'f' uses the order in the given file</span>
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2357
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<pre style="margin: 0;">+<span id="LC2357" class="line" lang="plaintext">(named in the last argument).</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="plaintext">.TP</span>
</pre>
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2359
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<pre style="margin: 0;">+<span id="LC2359" class="line" lang="plaintext">\fB\-\-king\-table\-filter\fR <min></span>
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2360
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<pre style="margin: 0;">+<span id="LC2360" class="line" lang="plaintext">: Specify minimum kinship coefficient for</span>
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2361
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<pre style="margin: 0;">+<span id="LC2361" class="line" lang="plaintext">inclusion in \fB\-\-make\-king\-table\fR report.</span>
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2362
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<pre style="margin: 0;">+<span id="LC2362" class="line" lang="plaintext">.TP</span>
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2363
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<pre style="margin: 0;">+<span id="LC2363" class="line" lang="plaintext">\fB\-\-king\-table\-subset\fR <f> [kmin] : Restrict current \fB\-\-make\-king\-table\fR run to</span>
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2364
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<pre style="margin: 0;">+<span id="LC2364" class="line" lang="plaintext">sample pairs listed in the given .kin0 file.</span>
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2365
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<pre style="margin: 0;">+<span id="LC2365" class="line" lang="plaintext">If a second argument is provided, only</span>
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2366
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<pre style="margin: 0;">+<span id="LC2366" class="line" lang="plaintext">sample pairs with kinship >= that threshold</span>
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2367
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<pre style="margin: 0;">+<span id="LC2367" class="line" lang="plaintext">(in the input .kin0) are processed.</span>
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2368
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<pre style="margin: 0;">+<span id="LC2368" class="line" lang="plaintext">.HP</span>
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2369
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<pre style="margin: 0;">+<span id="LC2369" class="line" lang="plaintext">\fB\-\-condition\fR <variant ID> [{dominant | recessive}] ['multiallelic']</span>
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2370
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<pre style="margin: 0;">+<span id="LC2370" class="line" lang="plaintext">.HP</span>
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2371
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<pre style="margin: 0;">+<span id="LC2371" class="line" lang="plaintext">\fB\-\-condition\-list\fR <fname> [{dominant | recessive}] ['multiallelic'] :</span>
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2372
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<pre style="margin: 0;">+<span id="LC2372" class="line" lang="plaintext">.IP</span>
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2373
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<pre style="margin: 0;">+<span id="LC2373" class="line" lang="plaintext">Add the given variant, or all variants in the given file, as \fB\-\-glm\fR</span>
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2374
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<pre style="margin: 0;">+<span id="LC2374" class="line" lang="plaintext">covariates.</span>
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2375
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<pre style="margin: 0;">+<span id="LC2375" class="line" lang="plaintext">By default, this errors out if any of the variants are multiallelic; add</span>
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2376
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<pre style="margin: 0;">+<span id="LC2376" class="line" lang="plaintext">the 'multiallelic' ('m' for short) modifier to allow them. They'll</span>
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2377
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<pre style="margin: 0;">+<span id="LC2377" class="line" lang="plaintext">effectively be split against the major allele (unless \fB\-\-glm\fR's 'omit\-ref'</span>
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2378
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<pre style="margin: 0;">+<span id="LC2378" class="line" lang="plaintext">modifier was specified), and all induced covariate names\-\-even for</span>
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2379
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<pre style="margin: 0;">+<span id="LC2379" class="line" lang="plaintext">biallelic variants\-\-will have an underscore followed by the allele code at</span>
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2380
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<pre style="margin: 0;">+<span id="LC2380" class="line" lang="plaintext">the end.</span>
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2381
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<pre style="margin: 0;">+<span id="LC2381" class="line" lang="plaintext">.TP</span>
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2382
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<pre style="margin: 0;">+<span id="LC2382" class="line" lang="plaintext">\fB\-\-parameters\fR <...> : Include only the given covariates/interactions in the</span>
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2383
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<pre style="margin: 0;">+<span id="LC2383" class="line" lang="plaintext">\fB\-\-glm\fR model, identified by a list of 1\-based indices</span>
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2384
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<pre style="margin: 0;">+<span id="LC2384" class="line" lang="plaintext">and/or ranges of them.</span>
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2385
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<pre style="margin: 0;">+<span id="LC2385" class="line" lang="plaintext">.TP</span>
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2386
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<pre style="margin: 0;">+<span id="LC2386" class="line" lang="plaintext">\fB\-\-tests\fR <...></span>
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<td class="diff-line-num new new_line" data-linenumber="2387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2387
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<pre style="margin: 0;">+<span id="LC2387" class="line" lang="plaintext">: Perform a (joint) test on the specified term(s) in the</span>
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2388
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<pre style="margin: 0;">+<span id="LC2388" class="line" lang="plaintext">.TP</span>
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2389
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="plaintext">\fB\-\-tests\fR all \fB\-\-glm\fR model, identified by 1\-based indices and/or ranges</span>
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2390
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<pre style="margin: 0;">+<span id="LC2390" class="line" lang="plaintext">of them.</span>
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2391
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<pre style="margin: 0;">+<span id="LC2391" class="line" lang="plaintext">* Note that, when \fB\-\-parameters\fR is also present, the</span>
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2392
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<pre style="margin: 0;">+<span id="LC2392" class="line" lang="plaintext">.TP</span>
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2393
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<pre style="margin: 0;">+<span id="LC2393" class="line" lang="plaintext">indices refer to the terms remaining AFTER pruning by</span>
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2394
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<pre style="margin: 0;">+<span id="LC2394" class="line" lang="plaintext">\fB\-\-parameters\fR.</span>
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2395
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<pre style="margin: 0;">+<span id="LC2395" class="line" lang="plaintext">.IP</span>
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2396
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<pre style="margin: 0;">+<span id="LC2396" class="line" lang="plaintext">* You can use '\-\-tests all' to include all terms.</span>
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2397
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<pre style="margin: 0;">+<span id="LC2397" class="line" lang="plaintext">.TP</span>
</pre>
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2398
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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="plaintext">\fB\-\-vif\fR <max VIF></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="plaintext">: Set VIF threshold for \fB\-\-glm\fR multicollinearity check</span>
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2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="plaintext">(default 50). (This is no longer skipped for</span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="plaintext">case/control phenotypes.)</span>
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<td class="diff-line-num new new_line" data-linenumber="2402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2403
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<pre style="margin: 0;">+<span id="LC2403" class="line" lang="plaintext">\fB\-\-max\-corr\fR <val></span>
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<td class="diff-line-num new new_line" data-linenumber="2404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2404
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<pre style="margin: 0;">+<span id="LC2404" class="line" lang="plaintext">: Skip \fB\-\-glm\fR regression when the absolute value of the</span>
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<td class="diff-line-num new new_line" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2405
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<pre style="margin: 0;">+<span id="LC2405" class="line" lang="plaintext">correlation between two predictors exceeds this value</span>
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2406
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<pre style="margin: 0;">+<span id="LC2406" class="line" lang="plaintext">(default 0.999).</span>
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2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="plaintext">.TP</span>
</pre>
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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="plaintext">\fB\-\-xchr\-model\fR <m></span>
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2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="plaintext">: Set the chrX \fB\-\-glm\fR/\-\-condition[\-list]/\-\-[v]score model.</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="plaintext">* '0' = skip chrX.</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="plaintext">* '1' = add sex as a covar on chrX, code males 0..1.</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="plaintext">* '2' (default) = chrX sex covar, code males 0..2.</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="plaintext">(Use the \fB\-\-glm\fR 'interaction' modifier to test for</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="plaintext">interaction between genotype and sex.)</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="plaintext">.HP</span>
</pre>
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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="plaintext">\fB\-\-adjust\fR ['zs'] ['gc'] ['log10'] ['cols='<column set descriptor>] :</span>
</pre>
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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="plaintext">.IP</span>
</pre>
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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="plaintext">For each association test in this run, report some basic multiple\-testing</span>
</pre>
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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="plaintext">corrections, sorted in increasing\-p\-value order. Modifiers work the same</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2420
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<pre style="margin: 0;">+<span id="LC2420" class="line" lang="plaintext">way as they do on \fB\-\-adjust\-file\fR.</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-lambda\fR</span>
</pre>
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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="plaintext">: Set genomic control lambda for \fB\-\-adjust[\-file]\fR.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2424
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<pre style="margin: 0;">+<span id="LC2424" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<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="plaintext">\fB\-\-adjust\-chr\-field\fR <n...></span>
</pre>
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</td>
<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="plaintext">: Set \fB\-\-adjust\-file\fR input field names. When</span>
</pre>
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</td>
<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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-adjust\-pos\-field\fR <n...></span>
</pre>
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</td>
<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="plaintext">multiple arguments are given to these flags,</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">\fB\-\-adjust\-id\-field\fR <n...></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">earlier names take precedence over later ones.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<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="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2434
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<pre style="margin: 0;">+<span id="LC2434" class="line" lang="plaintext">\fB\-\-adjust\-ref\-field\fR <n...></span>
</pre>
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2435
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<pre style="margin: 0;">+<span id="LC2435" class="line" lang="plaintext">.HP</span>
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2436
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<pre style="margin: 0;">+<span id="LC2436" class="line" lang="plaintext">\fB\-\-adjust\-alt\-field\fR <n...></span>
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2437
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<pre style="margin: 0;">+<span id="LC2437" class="line" lang="plaintext">.HP</span>
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2438
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<pre style="margin: 0;">+<span id="LC2438" class="line" lang="plaintext">\fB\-\-adjust\-a1\-field\fR <n...></span>
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2439
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<pre style="margin: 0;">+<span id="LC2439" class="line" lang="plaintext">.HP</span>
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2440
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<pre style="margin: 0;">+<span id="LC2440" class="line" lang="plaintext">\fB\-\-adjust\-test\-field\fR <n...></span>
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2441
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<pre style="margin: 0;">+<span id="LC2441" class="line" lang="plaintext">.HP</span>
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2442
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<pre style="margin: 0;">+<span id="LC2442" class="line" lang="plaintext">\fB\-\-adjust\-p\-field\fR <n...></span>
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2443
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<pre style="margin: 0;">+<span id="LC2443" class="line" lang="plaintext">.TP</span>
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2444
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<pre style="margin: 0;">+<span id="LC2444" class="line" lang="plaintext">\fB\-\-ci\fR <size></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="plaintext">: Report confidence ratios for odds ratios/betas.</span>
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2446
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<pre style="margin: 0;">+<span id="LC2446" class="line" lang="plaintext">.TP</span>
</pre>
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2447
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<pre style="margin: 0;">+<span id="LC2447" class="line" lang="plaintext">\fB\-\-pfilter\fR <val></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="plaintext">: Filter out assoc. test results with higher p\-values.</span>
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2449
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<pre style="margin: 0;">+<span id="LC2449" class="line" lang="plaintext">.TP</span>
</pre>
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2450
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<pre style="margin: 0;">+<span id="LC2450" class="line" lang="plaintext">\fB\-\-score\-col\-nums\fR <...> : Process all the specified coefficient columns in the</span>
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2451
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<pre style="margin: 0;">+<span id="LC2451" class="line" lang="plaintext">\fB\-\-score\fR file, identified by 1\-based indexes and/or</span>
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2452
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<pre style="margin: 0;">+<span id="LC2452" class="line" lang="plaintext">ranges of them.</span>
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2453
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<pre style="margin: 0;">+<span id="LC2453" class="line" lang="plaintext">.HP</span>
</pre>
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2454
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<pre style="margin: 0;">+<span id="LC2454" class="line" lang="plaintext">\fB\-\-q\-score\-range\fR <range file> <data file> [i] [j] ['header'] ['min'] :</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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2456
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<pre style="margin: 0;">+<span id="LC2456" class="line" lang="plaintext">Apply \fB\-\-score\fR to subset(s) of variants in the primary score list(s) based</span>
</pre>
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2457
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<pre style="margin: 0;">+<span id="LC2457" class="line" lang="plaintext">on e.g. p\-value ranges.</span>
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2458
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<pre style="margin: 0;">+<span id="LC2458" class="line" lang="plaintext">* The first file should have range labels in the first column, p\-value</span>
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2459
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<pre style="margin: 0;">+<span id="LC2459" class="line" lang="plaintext">.IP</span>
</pre>
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2460
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<pre style="margin: 0;">+<span id="LC2460" class="line" lang="plaintext">lower bounds in the second column, and upper bounds in the third column.</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="plaintext">Lines with too few entries, or nonnumeric values in the second or third</span>
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2462
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<pre style="margin: 0;">+<span id="LC2462" class="line" lang="plaintext">column, are ignored.</span>
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2463
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<pre style="margin: 0;">+<span id="LC2463" class="line" lang="plaintext">.IP</span>
</pre>
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2464
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<pre style="margin: 0;">+<span id="LC2464" class="line" lang="plaintext">* The second file should contain a variant ID and a p\-value on each line</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="plaintext">.TP</span>
</pre>
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2466
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<pre style="margin: 0;">+<span id="LC2466" class="line" lang="plaintext">(except possibly the first).</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="plaintext">Variant IDs are read from column #i and</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="plaintext">.IP</span>
</pre>
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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="plaintext">p\-values are read from column #j, where i defaults to 1 and j defaults to</span>
</pre>
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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="plaintext">i+1. The 'header' modifier causes the first nonempty line of this file</span>
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2471
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<pre style="margin: 0;">+<span id="LC2471" class="line" lang="plaintext">to be skipped.</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="plaintext">.IP</span>
</pre>
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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="plaintext">* By default, \fB\-\-q\-score\-range\fR errors out when a variant ID appears multiple</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">times in the data file (and is also present in the main dataset).</span>
</pre>
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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="plaintext">To use</span>
</pre>
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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="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2478
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<pre style="margin: 0;">+<span id="LC2478" class="line" lang="plaintext">the minimum p\-value in this case instead, add the 'min' modifier.</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="plaintext">.TP</span>
</pre>
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2480
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<pre style="margin: 0;">+<span id="LC2480" class="line" lang="plaintext">\fB\-\-vscore\-col\-nums\fR <...> : Process all the specified coefficient columns in</span>
</pre>
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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="plaintext">the \fB\-\-variant\-score\fR file, identified by 1\-based</span>
</pre>
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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="plaintext">indexes and/or ranges of them.</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-parallel\fR <k> <n> : Divide the output matrix into n pieces, and only compute</span>
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2485
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<pre style="margin: 0;">+<span id="LC2485" class="line" lang="plaintext">the kth piece. The primary output file will have the</span>
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2486
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<pre style="margin: 0;">+<span id="LC2486" class="line" lang="plaintext">piece number included in its name, e.g. plink2.king.13</span>
</pre>
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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="plaintext">or plink2.king.13.zst if k is 13. Concatenating these</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="plaintext">files in order will yield the full matrix of interest.</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="plaintext">(Yes, this can be done before decompression.)</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="plaintext">N.B. This generally cannot be used to directly write a</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="plaintext">symmetric square matrix. Choose square0 or triangle</span>
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2492
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<pre style="margin: 0;">+<span id="LC2492" class="line" lang="plaintext">shape instead, and postprocess as necessary.</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="plaintext">.TP</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="plaintext">\fB\-\-memory\fR <val> ['require'] : Set size, in MiB, of initial workspace malloc</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="plaintext">attempt. To error out instead of reducing the</span>
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<td class="diff-line-num new new_line" data-linenumber="2496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2496
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<pre style="margin: 0;">+<span id="LC2496" class="line" lang="plaintext">request size when the initial attempt fails, add</span>
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2497
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<pre style="margin: 0;">+<span id="LC2497" class="line" lang="plaintext">the 'require' modifier.</span>
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2498
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<pre style="margin: 0;">+<span id="LC2498" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2499
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<pre style="margin: 0;">+<span id="LC2499" class="line" lang="plaintext">\fB\-\-threads\fR <val></span>
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<td class="diff-line-num new new_line" data-linenumber="2500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2500
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<pre style="margin: 0;">+<span id="LC2500" class="line" lang="plaintext">: Set maximum number of compute threads.</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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-d\fR <char></span>
</pre>
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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="plaintext">: Change variant/covariate range delimiter (normally '\-').</span>
</pre>
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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="plaintext">.TP</span>
</pre>
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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="plaintext">\fB\-\-seed\fR <val...></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="plaintext">: Set random number seed(s). Each value must be an</span>
</pre>
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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="plaintext">integer between 0 and 4294967295 inclusive.</span>
</pre>
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2508
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<pre style="margin: 0;">+<span id="LC2508" class="line" lang="plaintext">Note that \fB\-\-threads\fR and "\-\-memory require" may also be</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="plaintext">needed to reproduce some randomized runs.</span>
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2510
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<pre style="margin: 0;">+<span id="LC2510" class="line" lang="plaintext">.TP</span>
</pre>
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2511
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<pre style="margin: 0;">+<span id="LC2511" class="line" lang="plaintext">\fB\-\-output\-min\-p\fR <p> : Specify minimum p\-value to write to reports.</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="plaintext">(2.23e\-308</span>
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<td class="diff-line-num new new_line" data-linenumber="2513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2513
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<pre style="margin: 0;">+<span id="LC2513" class="line" lang="plaintext">is useful for preventing underflow in some programs.)</span>
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<td class="diff-line-num new new_line" data-linenumber="2514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2514
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<pre style="margin: 0;">+<span id="LC2514" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2515
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<pre style="margin: 0;">+<span id="LC2515" class="line" lang="plaintext">\fB\-\-debug\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="2516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2516
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<pre style="margin: 0;">+<span id="LC2516" class="line" lang="plaintext">: Use slower, more crash\-resistant logging method.</span>
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<td class="diff-line-num new new_line" data-linenumber="2517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2517
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<pre style="margin: 0;">+<span id="LC2517" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2518
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<pre style="margin: 0;">+<span id="LC2518" class="line" lang="plaintext">\fB\-\-randmem\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2519
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<pre style="margin: 0;">+<span id="LC2519" class="line" lang="plaintext">: Randomize initial workspace memory (helps catch</span>
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<td class="diff-line-num new new_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2520
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<pre style="margin: 0;">+<span id="LC2520" class="line" lang="plaintext">uninitialized\-memory bugs).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2521
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<pre style="margin: 0;">+<span id="LC2521" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2522
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<pre style="margin: 0;">+<span id="LC2522" class="line" lang="plaintext">\fB\-\-warning\-errcode\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2523
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<pre style="margin: 0;">+<span id="LC2523" class="line" lang="plaintext">: Return a nonzero error code to the OS when a run</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2524
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<pre style="margin: 0;">+<span id="LC2524" class="line" lang="plaintext">completes with warning(s).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2525
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<pre style="margin: 0;">+<span id="LC2525" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2526
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<pre style="margin: 0;">+<span id="LC2526" class="line" lang="plaintext">\fB\-\-zst\-level\fR <lvl></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2527
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<pre style="margin: 0;">+<span id="LC2527" class="line" lang="plaintext">: Set the Zstd compression level (1\-22, default 3).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2528
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<pre style="margin: 0;">+<span id="LC2528" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2529
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<pre style="margin: 0;">+<span id="LC2529" class="line" lang="plaintext">Primary methods paper:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2530
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<pre style="margin: 0;">+<span id="LC2530" class="line" lang="plaintext">Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2531
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<pre style="margin: 0;">+<span id="LC2531" class="line" lang="plaintext">Second\-generation PLINK: rising to the challenge of larger and richer datasets.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2532
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<pre style="margin: 0;">+<span id="LC2532" class="line" lang="plaintext">GigaScience, 4.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2533
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<pre style="margin: 0;">+<span id="LC2533" class="line" lang="plaintext">.SH "SEE ALSO"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2534
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<pre style="margin: 0;">+<span id="LC2534" class="line" lang="plaintext">The full documentation for</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2535
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<pre style="margin: 0;">+<span id="LC2535" class="line" lang="plaintext">.B PLINK v2.00a3 64-bit (9 Apr</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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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<td class="diff-line-num new new_line" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2536
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<pre style="margin: 0;">+<span id="LC2536" class="line" lang="plaintext">is maintained as a Texinfo manual. If the</span>
</pre>
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<pre style="margin: 0;">+<span id="LC2537" class="line" lang="plaintext">.B info</span>
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2538
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<pre style="margin: 0;">+<span id="LC2538" class="line" lang="plaintext">and</span>
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2539
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<pre style="margin: 0;">+<span id="LC2539" class="line" lang="plaintext">.B PLINK v2.00a3 64-bit (9 Apr</span>
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2540
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<pre style="margin: 0;">+<span id="LC2540" class="line" lang="plaintext">programs are properly installed at your site, the command</span>
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2541
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<pre style="margin: 0;">+<span id="LC2541" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC2542" class="line" lang="plaintext">.B info PLINK v2.00a3 64-bit (9 Apr</span>
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2543
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<pre style="margin: 0;">+<span id="LC2543" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC2544" class="line" lang="plaintext">should give you access to the complete manual.</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/7f9b980e5aefd8fa948ab9571a95ce7ebc1c4bc5...01274352f062d9c7b637cba5d737dcefc3d23012#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">@@ -14,11 +14,13 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> help2man --no-discard-stderr --name="whole genome SNP analysis" $(DIRECTORY)/plink2 > plink2.1</span>
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<pre style="margin: 0;">+<span id="LC17" 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="LC18" class="line" lang="plaintext"># which lead to several lintian warnings</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"># help2man --no-discard-stderr --name="whole genome SNP analysis" $(DIRECTORY)/plink2 > plink2.1</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" $(DIRECTORY)/pgen_compress > pgen_compress.1</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh_installman plink2.1</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> dh_installman <span class="idiff left right">debian/</span>plink2.1</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> dh_installman pgen_compress.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_installchangelogs:</span>
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