Update bcftools/roh and roh-viz documentation

doc/bcftools.1

@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHOR(S)" section]
 .\" Generator: Asciidoctor 2.0.15.dev
-.\"      Date: 2024-12-16
+.\"      Date: 2024-12-28
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2024-12-16" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2024-12-28" "\ \&" "\ \&"
 .ie \n(.g .ds Aq \(aq
 .el       .ds Aq '
 .ss \n[.ss] 0
@@ -51,7 +51,7 @@ standard input (stdin) and outputs to the standard output (stdout). Several
 commands can thus be  combined  with  Unix pipes.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2024\-12\-16 09:31 GMT\fP and refers to bcftools git version \fB1.21\-58\-g6559a12a+\fP.
+This manual page was last updated \fB2024\-12\-28 22:19 GMT\fP and refers to bcftools git version \fB1.21\-61\-g68f13f2e+\fP.
 .SS "BCF1"
 .sp
 The obsolete BCF1 format output by versions of samtools <= 0.1.19 is \fBnot\fP
@@ -347,7 +347,7 @@ Some helper scripts are bundled with the bcftools code.
 .  sp -1
 .  IP \(bu 2.3
 .\}
-\fBgff2gff\fP  .. converts a GFF file to the format required by \fBcsq\fP
+\fBgff2gff\fP  .. converts a GFF file to the format required by \fBbcftools csq\fP
 .RE
 .sp
 .RS 4
@@ -358,7 +358,18 @@ Some helper scripts are bundled with the bcftools code.
 .  sp -1
 .  IP \(bu 2.3
 .\}
-\fBplot\-vcfstats\fP  .. plots the output of \fBstats\fP
+\fBplot\-vcfstats\fP  .. plots the output of \fBbcftools stats\fP
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.  sp -1
+.  IP \(bu 2.3
+.\}
+\fBroh\-viz\fP .. creates HTML/JavaScript visualization of \fBbcftools roh\fP
 .RE
 .SH "COMMANDS AND OPTIONS"
 .SS "Common Options"
@@ -5079,7 +5090,8 @@ see \fBCommon Options\fP
 .SS "bcftools roh [\fIOPTIONS\fP] \fIfile.vcf.gz\fP"
 .sp
 A program for detecting runs of homo/autozygosity. Only bi\-allelic sites
-are considered.
+are considered. The results can be visualized in HTML/JavaScript using
+the \fBroh\-viz\fP script.
 .SS "The HMM model:"
 .sp
 .if n .RS 4
@@ -5836,6 +5848,64 @@ cd outdir && python plot.py && pdflatex summary.tex
 .fam
 .fi
 .if n .RE
+.SS "roh\-viz [\fIOPTIONS\fP]"
+.sp
+Script for visualizing the output of \fBbcftools roh\fP. It creates
+a HTML/JavaScript document which can be interactively viewed in your favorite
+web browser.
+.sp
+\fB\-i, \-\-RoH\-file\fP \fIFILE\fP
+.RS 4
+Output of bcftools/roh
+.RE
+.sp
+\fB\-l, \-\-min\-length\fP \fINUM\fP
+.RS 4
+Mimimum length of ROH [1e6]
+.RE
+.sp
+\fB\-o, \-\-output\fP \fIFILE\fP
+.RS 4
+HTML output file
+.RE
+.sp
+\fB\-r, \-\-regions\fP \fILIST\fP
+.RS 4
+List of chromosomes/regions
+.RE
+.sp
+\fB\-s, \-\-samples\fP \fILIST\fP
+.RS 4
+List of samples to show
+.RE
+.sp
+\fB\-v, \-\-VCF\-file\fP \fIFILE\fP
+.RS 4
+VCF file to determine homozygosity rate
+.RE
+.sp
+\fB\-h, \-?, \-\-help\fP
+This help message
+.sp
+\fBExample:\fP
+.sp
+.if n .RS 4
+.nf
+.fam C
+# Find RoH regions
+bcftools roh \-\-AF\-dflt 0.5 \-G 30 \-Or \-o roh.txt file.bcf
+.fam
+.fi
+.if n .RE
+.sp
+.if n .RS 4
+.nf
+.fam C
+# Create HTML/JavaScript visualization
+roh\-viz \-r roh.txt \-v file.bcf \-o output.html
+.fam
+.fi
+.if n .RE
 .SH "FILTERING EXPRESSIONS"
 .sp
 These filtering expressions are accepted by most of the commands.

doc/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>

doc/bcftools.txt

@@ -109,8 +109,9 @@ LIST OF SCRIPTS
 ---------------
 Some helper scripts are bundled with the bcftools code.
 
-- *<<gff2gff,gff2gff>>*  .. converts a GFF file to the format required by *<<csq,csq>>*
-- *<<plot-vcfstats,plot-vcfstats>>*  .. plots the output of *<<stats,stats>>*
+- *<<gff2gff,gff2gff>>*  .. converts a GFF file to the format required by *<<csq,bcftools csq>>*
+- *<<plot-vcfstats,plot-vcfstats>>*  .. plots the output of *<<stats,bcftools stats>>*
+- *<<roh-viz,roh-viz>>* .. creates HTML/JavaScript visualization of *<<roh,bcftools roh>>*
 
 
 COMMANDS AND OPTIONS
@@ -3286,7 +3287,8 @@ Modify header of VCF/BCF files, change sample names.
 [[roh]]
 === bcftools roh ['OPTIONS'] 'file.vcf.gz'
 A program for detecting runs of homo/autozygosity. Only bi-allelic sites
-are considered.
+are considered. The results can be visualized in HTML/JavaScript using
+the *<<roh-viz,roh-viz>>* script.
 
 ==== The HMM model:
 --------------------------------------
@@ -3829,6 +3831,44 @@ chromosome separately), plots graphs and creates a PDF presentation.
 --
 
 
+[[roh-viz]]
+=== roh-viz ['OPTIONS']
+Script for visualizing the output of *<<roh,bcftools roh>>*. It creates
+a HTML/JavaScript document which can be interactively viewed in your favorite
+web browser.
+
+*-i, --RoH-file* 'FILE'::
+    Output of bcftools/roh
+
+*-l, --min-length* 'NUM'::
+    Mimimum length of ROH [1e6]
+
+*-o, --output* 'FILE'::
+    HTML output file
+
+*-r, --regions* 'LIST'::
+    List of chromosomes/regions
+
+*-s, --samples* 'LIST'::
+    List of samples to show
+
+*-v, --VCF-file* 'FILE'::
+    VCF file to determine homozygosity rate
+
+*-h, -?, --help*
+    This help message
+
+
+*Example:*
+--
+    # Find RoH regions
+    bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt file.bcf
+
+    # Create HTML/JavaScript visualization
+    roh-viz -r roh.txt -v file.bcf -o output.html
+--
+
+
 [[expressions]]
 FILTERING EXPRESSIONS
 ---------------------

misc/roh-viz

@@ -54,7 +54,7 @@ sub error
         "   -v, --VCF-file FILE     VCF file to determine homozygosity rate\n",
         "   -h, -?, --help          This help message\n",
         "Example:\n",
-        "   bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt file.bcf",
+        "   bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt file.bcf\n",
         "   roh-viz -r roh.txt -v file.bcf -o output.html\n",
         "\n";
     exit -1;