diff --git a/doc/bcftools.1 b/doc/bcftools.1 index 480ee9c3..ceb6bd7e 100644 --- a/doc/bcftools.1 +++ b/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. diff --git a/doc/bcftools.html b/doc/bcftools.html index 87533bad..eb8b1cbe 100644 --- a/doc/bcftools.html +++ b/doc/bcftools.html @@ -50,7 +50,7 @@

DESCRIPTION

VERSION

-

This manual page was last updated 2024-12-16 09:31 GMT and refers to bcftools git version 1.21-58-g6559a12a+.

+

This manual page was last updated 2024-12-28 22:19 GMT and refers to bcftools git version 1.21-61-g68f13f2e+.

@@ -178,10 +178,13 @@

LIST OF SCRIPTS

@@ -4380,7 +4383,8 @@

bcftools reheader [OPTIONS] file.vcf.gz

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 script.

The HMM model:

@@ -5114,6 +5118,65 @@

plot-vcfstats [OPTIONS] file.vchk [R

+
+

roh-viz [OPTIONS]

+
+

Script for visualizing the output of 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
+
+
+
+
+
@@ -5654,7 +5717,7 @@

COPYING

diff --git a/doc/bcftools.txt b/doc/bcftools.txt index 21f6c5b6..713a1902 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -109,8 +109,9 @@ LIST OF SCRIPTS --------------- Some helper scripts are bundled with the bcftools code. -- *<>* .. converts a GFF file to the format required by *<>* -- *<>* .. plots the output of *<>* +- *<>* .. converts a GFF file to the format required by *<>* +- *<>* .. plots the output of *<>* +- *<>* .. creates HTML/JavaScript visualization of *<>* 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 *<>* 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 *<>*. 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 --------------------- diff --git a/misc/roh-viz b/misc/roh-viz index 694ec3f0..78b05bd7 100755 --- a/misc/roh-viz +++ b/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;