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Update bcftools/roh and roh-viz documentation
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‎doc/bcftools.1‎

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

‎doc/bcftools.html‎

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

‎doc/bcftools.txt‎

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---------------
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Some helper scripts are bundled with the bcftools code.
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- *<<gff2gff,gff2gff>>* .. converts a GFF file to the format required by *<<csq,csq>>*
113-
- *<<plot-vcfstats,plot-vcfstats>>* .. plots the output of *<<stats,stats>>*
112+
- *<<gff2gff,gff2gff>>* .. converts a GFF file to the format required by *<<csq,bcftools csq>>*
113+
- *<<plot-vcfstats,plot-vcfstats>>* .. plots the output of *<<stats,bcftools stats>>*
114+
- *<<roh-viz,roh-viz>>* .. creates HTML/JavaScript visualization of *<<roh,bcftools roh>>*
114115

115116

116117
COMMANDS AND OPTIONS
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32863287
[[roh]]
32873288
=== bcftools roh ['OPTIONS'] 'file.vcf.gz'
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A program for detecting runs of homo/autozygosity. Only bi-allelic sites
3289-
are considered.
3290+
are considered. The results can be visualized in HTML/JavaScript using
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the *<<roh-viz,roh-viz>>* script.
32903292

32913293
==== The HMM model:
32923294
--------------------------------------
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38293831
--
38303832

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3834+
[[roh-viz]]
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=== roh-viz ['OPTIONS']
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Script for visualizing the output of *<<roh,bcftools roh>>*. It creates
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a HTML/JavaScript document which can be interactively viewed in your favorite
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web browser.
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*-i, --RoH-file* 'FILE'::
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Output of bcftools/roh
3842+
3843+
*-l, --min-length* 'NUM'::
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Mimimum length of ROH [1e6]
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3846+
*-o, --output* 'FILE'::
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HTML output file
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3849+
*-r, --regions* 'LIST'::
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List of chromosomes/regions
3851+
3852+
*-s, --samples* 'LIST'::
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List of samples to show
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3855+
*-v, --VCF-file* 'FILE'::
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VCF file to determine homozygosity rate
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3858+
*-h, -?, --help*
3859+
This help message
3860+
3861+
3862+
*Example:*
3863+
--
3864+
# Find RoH regions
3865+
bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt file.bcf
3866+
3867+
# Create HTML/JavaScript visualization
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roh-viz -r roh.txt -v file.bcf -o output.html
3869+
--
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38323872
[[expressions]]
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FILTERING EXPRESSIONS
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---------------------

‎misc/roh-viz‎

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" -v, --VCF-file FILE VCF file to determine homozygosity rate\n",
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" -h, -?, --help This help message\n",
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"Example:\n",
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" bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt file.bcf",
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" bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt file.bcf\n",
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" roh-viz -r roh.txt -v file.bcf -o output.html\n",
5959
"\n";
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exit -1;

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