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Add tips on performance and scaling
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pd3 committed Apr 8, 2024
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5 changes: 4 additions & 1 deletion howtos/FAQ.html
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<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 2.0.16">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Frequently Asked Questions</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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3 changes: 3 additions & 0 deletions howtos/annotate.html
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
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<p><a href="plugins.html">Plugins</a></p>
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<li>
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5 changes: 4 additions & 1 deletion howtos/cnv-calling.html
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<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 2.0.16">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Copy Number Variation</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
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<p><a href="plugins.html">Plugins</a></p>
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5 changes: 4 additions & 1 deletion howtos/consensus-sequence.html
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<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 2.0.16">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Consensus sequence</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
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<p><a href="plugins.html">Plugins</a></p>
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<li>
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9 changes: 6 additions & 3 deletions howtos/convert.html
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<html lang="en">
<head>
<meta charset="UTF-8">
<!--[if IE]><meta http-equiv="X-UA-Compatible" content="IE=edge"><![endif]-->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 1.5.2">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Converting from 23andMe to VCF</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
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<li>
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<div class="sect2">
<h3 id="_feedback">Feedback</h3>
<div class="paragraph">
<p>We welcome your feedback, please help us improve this page by
<p>We welcome your feedback, please help us improve this page by
either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending
a pull request.</p>
</div>
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9 changes: 6 additions & 3 deletions howtos/csq-calling.html
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<html lang="en">
<head>
<meta charset="UTF-8">
<!--[if IE]><meta http-equiv="X-UA-Compatible" content="IE=edge"><![endif]-->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 1.5.2">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Consequence calling</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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<div class="sect2">
<h3 id="_feedback">Feedback</h3>
<div class="paragraph">
<p>We welcome your feedback, please help us improve this page by
<p>We welcome your feedback, please help us improve this page by
either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending
a pull request.</p>
</div>
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9 changes: 6 additions & 3 deletions howtos/filtering.html
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<html lang="en">
<head>
<meta charset="UTF-8">
<!--[if IE]><meta http-equiv="X-UA-Compatible" content="IE=edge"><![endif]-->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 1.5.2">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Filtering</title>
<link rel="stylesheet" href="./index.css">
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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<div class="sect2">
<h3 id="_feedback">Feedback</h3>
<div class="paragraph">
<p>We welcome your feedback, please help us improve this page by
<p>We welcome your feedback, please help us improve this page by
either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending
a pull request.</p>
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1 change: 1 addition & 0 deletions howtos/header.inc
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* link:annotate.html[Adding annotation]
* link:query.html[Extracting information]
* link:filtering.html[Filtering expressions]
* link:scaling.html[Performance and Scaling]
* link:plugins.html[Plugins]
* link:FAQ.html[FAQ]

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9 changes: 6 additions & 3 deletions howtos/index.html
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<html lang="en">
<head>
<meta charset="UTF-8">
<!--[if IE]><meta http-equiv="X-UA-Compatible" content="IE=edge"><![endif]-->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 1.5.2">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>BCFtools HowTo</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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<div class="sect2">
<h3 id="_feedback">Feedback</h3>
<div class="paragraph">
<p>We welcome your feedback, please help us improve this page by
<p>We welcome your feedback, please help us improve this page by
either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending
a pull request.</p>
</div>
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3 changes: 3 additions & 0 deletions howtos/install.html
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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9 changes: 6 additions & 3 deletions howtos/plugin.af-dist.html
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<html lang="en">
<head>
<meta charset="UTF-8">
<!--[if IE]><meta http-equiv="X-UA-Compatible" content="IE=edge"><![endif]-->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 1.5.2">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Plugin af-dist</title>
<link rel="stylesheet" href="./index.css">
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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<div class="sect2">
<h3 id="_feedback">Feedback</h3>
<div class="paragraph">
<p>We welcome your feedback, please help us improve this page by
<p>We welcome your feedback, please help us improve this page by
either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending
a pull request.</p>
</div>
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9 changes: 6 additions & 3 deletions howtos/plugin.api.html
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<html lang="en">
<head>
<meta charset="UTF-8">
<!--[if IE]><meta http-equiv="X-UA-Compatible" content="IE=edge"><![endif]-->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 1.5.2">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Plugins for developers</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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<div class="sect2">
<h3 id="_feedback">Feedback</h3>
<div class="paragraph">
<p>We welcome your feedback, please help us improve this page by
<p>We welcome your feedback, please help us improve this page by
either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending
a pull request.</p>
</div>
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3 changes: 3 additions & 0 deletions howtos/plugin.fill-tags.html
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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9 changes: 6 additions & 3 deletions howtos/plugin.fixref.html
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<html lang="en">
<head>
<meta charset="UTF-8">
<!--[if IE]><meta http-equiv="X-UA-Compatible" content="IE=edge"><![endif]-->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 1.5.2">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Plugin fixref</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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<div class="sect2">
<h3 id="_feedback">Feedback</h3>
<div class="paragraph">
<p>We welcome your feedback, please help us improve this page by
<p>We welcome your feedback, please help us improve this page by
either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending
a pull request.</p>
</div>
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9 changes: 6 additions & 3 deletions howtos/plugin.mendelian.html
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<html lang="en">
<head>
<meta charset="UTF-8">
<!--[if IE]><meta http-equiv="X-UA-Compatible" content="IE=edge"><![endif]-->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 1.5.2">
<meta name="generator" content="Asciidoctor 2.0.15.dev">
<title>Plugin mendelian</title>
<link rel="stylesheet" href="./index.css">
</head>
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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<div class="sect2">
<h3 id="_feedback">Feedback</h3>
<div class="paragraph">
<p>We welcome your feedback, please help us improve this page by
<p>We welcome your feedback, please help us improve this page by
either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending
a pull request.</p>
</div>
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3 changes: 3 additions & 0 deletions howtos/plugin.split-vep.html
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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6 changes: 5 additions & 1 deletion howtos/plugin.tag2tag.html
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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<h2 id="_plugin_tag2tag">Plugin tag2tag</h2>
<div class="sectionbody">
<div class="paragraph">
<p>This plugin can be used to convert between similar tags such GL,PL,GP or QR,QA,QS or tags that use localized alleles, e.g. LPL,LAD.</p>
<p>This plugin can be used to convert between similar tags such GL,PL,GP or QR,QA,QS or tags that use local alleles, e.g. LPL,LAD.
(For a description of localized tags see <a href="scaling.html">the page on scaling</a>.)</p>
</div>
<div class="paragraph">
<p>The list of plugin-specific options can be obtained by running <code>bcftools +tag2tag -h</code>, which will print the following usage page:</p>
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3 changes: 2 additions & 1 deletion howtos/plugin.tag2tag.txt
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Plugin tag2tag
--------------

This plugin can be used to convert between similar tags such GL,PL,GP or QR,QA,QS or tags that use localized alleles, e.g. LPL,LAD.
This plugin can be used to convert between similar tags such GL,PL,GP or QR,QA,QS or tags that use local alleles, e.g. LPL,LAD.
(For a description of localized tags see link:scaling.html[the page on scaling].)

The list of plugin-specific options can be obtained by running `bcftools +tag2tag -h`, which will print the following usage page:
----
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3 changes: 3 additions & 0 deletions howtos/plugin.trio-dnm2.html
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<p><a href="filtering.html">Filtering expressions</a></p>
</li>
<li>
<p><a href="scaling.html">Performance and Scaling</a></p>
</li>
<li>
<p><a href="plugins.html">Plugins</a></p>
</li>
<li>
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