Update roh documentation

samtools · Dec 28, 2024 · b9f2edb · b9f2edb
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diff --git a/bcftools-man.html b/bcftools-man.html
@@ -50,7 +50,7 @@ <h2 id="_description">DESCRIPTION</h2>
 <div class="sect2">
 <h3 id="_version">VERSION</h3>
 <div class="paragraph">
-<p>This manual page was last updated <strong>2024-12-16 09:31 GMT</strong> and refers to bcftools git version <strong>1.21-58-g6559a12a+</strong>.</p>
+<p>This manual page was last updated <strong>2024-12-28 22:19 GMT</strong> and refers to bcftools git version <strong>1.21-61-g68f13f2e+</strong>.</p>
 </div>
 </div>
 <div class="sect2">
@@ -178,10 +178,13 @@ <h2 id="_list_of_scripts">LIST OF SCRIPTS</h2>
 <div class="ulist">
 <ul>
 <li>
-<p><strong><a href="#gff2gff">gff2gff</a></strong>  .. converts a GFF file to the format required by <strong><a href="#csq">csq</a></strong></p>
+<p><strong><a href="#gff2gff">gff2gff</a></strong>  .. converts a GFF file to the format required by <strong><a href="#csq">bcftools csq</a></strong></p>
 </li>
 <li>
-<p><strong><a href="#plot-vcfstats">plot-vcfstats</a></strong>  .. plots the output of <strong><a href="#stats">stats</a></strong></p>
+<p><strong><a href="#plot-vcfstats">plot-vcfstats</a></strong>  .. plots the output of <strong><a href="#stats">bcftools stats</a></strong></p>
+</li>
+<li>
+<p><strong><a href="#roh-viz">roh-viz</a></strong> .. creates HTML/JavaScript visualization of <strong><a href="#roh">bcftools roh</a></strong></p>
 </li>
 </ul>
 </div>
@@ -4380,7 +4383,8 @@ <h3 id="reheader">bcftools reheader [<em>OPTIONS</em>] <em>file.vcf.gz</em></h3>
 <h3 id="roh">bcftools roh [<em>OPTIONS</em>] <em>file.vcf.gz</em></h3>
 <div class="paragraph">
 <p>A program for detecting runs of homo/autozygosity. Only bi-allelic sites
-are considered.</p>
+are considered. The results can be visualized in HTML/JavaScript using
+the <strong><a href="#roh-viz">roh-viz</a></strong> script.</p>
 </div>
 <div class="sect3">
 <h4 id="_the_hmm_model">The HMM model:</h4>
@@ -5114,6 +5118,65 @@ <h3 id="plot-vcfstats">plot-vcfstats [<em>OPTIONS</em>] <em>file.vchk</em> [&#82
 </div>
 </div>
 </div>
+<div class="sect2">
+<h3 id="roh-viz">roh-viz [<em>OPTIONS</em>]</h3>
+<div class="paragraph">
+<p>Script for visualizing the output of <strong><a href="#roh">bcftools roh</a></strong>. It creates
+a HTML/JavaScript document which can be interactively viewed in your favorite
+web browser.</p>
+</div>
+<div class="dlist">
+<dl>
+<dt class="hdlist1"><strong>-i, --RoH-file</strong> <em>FILE</em></dt>
+<dd>
+<p>Output of bcftools/roh</p>
+</dd>
+<dt class="hdlist1"><strong>-l, --min-length</strong> <em>NUM</em></dt>
+<dd>
+<p>Mimimum length of ROH [1e6]</p>
+</dd>
+<dt class="hdlist1"><strong>-o, --output</strong> <em>FILE</em></dt>
+<dd>
+<p>HTML output file</p>
+</dd>
+<dt class="hdlist1"><strong>-r, --regions</strong> <em>LIST</em></dt>
+<dd>
+<p>List of chromosomes/regions</p>
+</dd>
+<dt class="hdlist1"><strong>-s, --samples</strong> <em>LIST</em></dt>
+<dd>
+<p>List of samples to show</p>
+</dd>
+<dt class="hdlist1"><strong>-v, --VCF-file</strong> <em>FILE</em></dt>
+<dd>
+<p>VCF file to determine homozygosity rate</p>
+</dd>
+</dl>
+</div>
+<div class="paragraph">
+<p><strong>-h, -?, --help</strong>
+    This help message</p>
+</div>
+<div class="paragraph">
+<p><strong>Example:</strong></p>
+</div>
+<div class="openblock">
+<div class="content">
+<div class="literalblock">
+<div class="content">
+<pre># Find RoH regions
+bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt file.bcf</pre>
+</div>
+</div>
+<div class="literalblock">
+<div class="content">
+<pre># Create HTML/JavaScript visualization
+roh-viz -r roh.txt -v file.bcf -o output.html</pre>
+</div>
+</div>
+</div>
+</div>
+</div>
 </div>
 </div>
 <div class="sect1">
@@ -5654,7 +5717,7 @@ <h2 id="_copying">COPYING</h2>
 </div>
 <div id="footer">
 <div id="footer-text">
-Last updated 2024-12-16 09:31:50 UTC
+Last updated 2024-12-28 22:19:33 UTC
 </div>
 </div>
 </body>

diff --git a/bcftools.html b/bcftools.html
@@ -50,7 +50,7 @@ <h2 id="_description">DESCRIPTION</h2>
 <div class="sect2">
 <h3 id="_version">VERSION</h3>
 <div class="paragraph">
-<p>This manual page was last updated <strong>2024-12-16 09:31 GMT</strong> and refers to bcftools git version <strong>1.21-58-g6559a12a+</strong>.</p>
+<p>This manual page was last updated <strong>2024-12-28 22:19 GMT</strong> and refers to bcftools git version <strong>1.21-61-g68f13f2e+</strong>.</p>
 </div>
 </div>
 <div class="sect2">
@@ -178,10 +178,13 @@ <h2 id="_list_of_scripts">LIST OF SCRIPTS</h2>
 <div class="ulist">
 <ul>
 <li>
-<p><strong><a href="#gff2gff">gff2gff</a></strong>  .. converts a GFF file to the format required by <strong><a href="#csq">csq</a></strong></p>
+<p><strong><a href="#gff2gff">gff2gff</a></strong>  .. converts a GFF file to the format required by <strong><a href="#csq">bcftools csq</a></strong></p>
 </li>
 <li>
-<p><strong><a href="#plot-vcfstats">plot-vcfstats</a></strong>  .. plots the output of <strong><a href="#stats">stats</a></strong></p>
+<p><strong><a href="#plot-vcfstats">plot-vcfstats</a></strong>  .. plots the output of <strong><a href="#stats">bcftools stats</a></strong></p>
+</li>
+<li>
+<p><strong><a href="#roh-viz">roh-viz</a></strong> .. creates HTML/JavaScript visualization of <strong><a href="#roh">bcftools roh</a></strong></p>
 </li>
 </ul>
 </div>
@@ -4380,7 +4383,8 @@ <h3 id="reheader">bcftools reheader [<em>OPTIONS</em>] <em>file.vcf.gz</em></h3>
 <h3 id="roh">bcftools roh [<em>OPTIONS</em>] <em>file.vcf.gz</em></h3>
 <div class="paragraph">
 <p>A program for detecting runs of homo/autozygosity. Only bi-allelic sites
-are considered.</p>
+are considered. The results can be visualized in HTML/JavaScript using
+the <strong><a href="#roh-viz">roh-viz</a></strong> script.</p>
 </div>
 <div class="sect3">
 <h4 id="_the_hmm_model">The HMM model:</h4>
@@ -5114,6 +5118,65 @@ <h3 id="plot-vcfstats">plot-vcfstats [<em>OPTIONS</em>] <em>file.vchk</em> [&#82
 </div>
 </div>
 </div>
+<div class="sect2">
+<h3 id="roh-viz">roh-viz [<em>OPTIONS</em>]</h3>
+<div class="paragraph">
+<p>Script for visualizing the output of <strong><a href="#roh">bcftools roh</a></strong>. It creates
+a HTML/JavaScript document which can be interactively viewed in your favorite
+web browser.</p>
+</div>
+<div class="dlist">
+<dl>
+<dt class="hdlist1"><strong>-i, --RoH-file</strong> <em>FILE</em></dt>
+<dd>
+<p>Output of bcftools/roh</p>
+</dd>
+<dt class="hdlist1"><strong>-l, --min-length</strong> <em>NUM</em></dt>
+<dd>
+<p>Mimimum length of ROH [1e6]</p>
+</dd>
+<dt class="hdlist1"><strong>-o, --output</strong> <em>FILE</em></dt>
+<dd>
+<p>HTML output file</p>
+</dd>
+<dt class="hdlist1"><strong>-r, --regions</strong> <em>LIST</em></dt>
+<dd>
+<p>List of chromosomes/regions</p>
+</dd>
+<dt class="hdlist1"><strong>-s, --samples</strong> <em>LIST</em></dt>
+<dd>
+<p>List of samples to show</p>
+</dd>
+<dt class="hdlist1"><strong>-v, --VCF-file</strong> <em>FILE</em></dt>
+<dd>
+<p>VCF file to determine homozygosity rate</p>
+</dd>
+</dl>
+</div>
+<div class="paragraph">
+<p><strong>-h, -?, --help</strong>
+    This help message</p>
+</div>
+<div class="paragraph">
+<p><strong>Example:</strong></p>
+</div>
+<div class="openblock">
+<div class="content">
+<div class="literalblock">
+<div class="content">
+<pre># Find RoH regions
+bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt file.bcf</pre>
+</div>
+</div>
+<div class="literalblock">
+<div class="content">
+<pre># Create HTML/JavaScript visualization
+roh-viz -r roh.txt -v file.bcf -o output.html</pre>
+</div>
+</div>
+</div>
+</div>
+</div>
 </div>
 </div>
 <div class="sect1">
@@ -5654,7 +5717,7 @@ <h2 id="_copying">COPYING</h2>
 </div>
 <div id="footer">
 <div id="footer-text">
-Last updated 2024-12-16 09:31:50 UTC
+Last updated 2024-12-28 22:19:33 UTC
 </div>
 </div>
 </body>

diff --git a/howtos/plugin.split-vep.html b/howtos/plugin.split-vep.html
@@ -4,7 +4,7 @@
 <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 2.0.20">
+<meta name="generator" content="Asciidoctor 2.0.15.dev">
 <title>Plugin split-vep</title>
 <link rel="stylesheet" href="./index.css">
 </head>

diff --git a/howtos/roh-calling.html b/howtos/roh-calling.html
@@ -131,7 +131,8 @@ <h3 id="_example_1">Example 1</h3>
 </div>
 <div class="listingblock">
 <div class="content">
-<pre>bcftools roh -G30 --AF-dflt 0.4 file.vcf</pre>
+<pre>bcftools roh -G30 --AF-dflt 0.4 file.vcf -o out.txt
+roh-viz -i out.txt -v test.vcf.gz -o rmme.html</pre>
 </div>
 </div>
 <div class="paragraph">

diff --git a/howtos/roh-calling.txt b/howtos/roh-calling.txt
@@ -45,7 +45,8 @@ and there is just one sample so it cannot be estimated on the fly. Hence we use
 a default AF value 0.4.
 
 ----
-bcftools roh -G30 --AF-dflt 0.4 file.vcf
+bcftools roh -G30 --AF-dflt 0.4 file.vcf -o out.txt
+roh-viz -i out.txt -v test.vcf.gz -o rmme.html
 ----
 
 Please check this link:roh-calling/usage-example.tgz[usage example] for details
@@ -148,7 +149,7 @@ program.  For example in this run many sites were filtered:
 Number of lines: total/processed: 599218/37730
 ----
 
-If the number of the processed sites is too low, check what was the reason for excluding 
+If the number of the processed sites is too low, check what was the reason for excluding
 them. This command should give the number of sites that were processed:
 
 ----

diff --git a/howtos/roh-calling/roh-example.png b/howtos/roh-calling/roh-example.png
diff --git a/howtos/variant-calling.html b/howtos/variant-calling.html
@@ -4,7 +4,7 @@
 <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 2.0.20">
+<meta name="generator" content="Asciidoctor 2.0.15.dev">
 <title>Variant calling</title>
 <link rel="stylesheet" href="./index.css">
 </head>