1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
|
'\" t
.TH samtools-tview 1 "12 September 2024" "samtools-1.21" "Bioinformatics tools"
.SH NAME
samtools tview \- display alignments in a curses-based interactive viewer.
.\"
.\" Copyright (C) 2008-2011, 2013-2019, 2022 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
.\" Permission is hereby granted, free of charge, to any person obtaining a
.\" copy of this software and associated documentation files (the "Software"),
.\" to deal in the Software without restriction, including without limitation
.\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
.\" and/or sell copies of the Software, and to permit persons to whom the
.\" Software is furnished to do so, subject to the following conditions:
.\"
.\" The above copyright notice and this permission notice shall be included in
.\" all copies or substantial portions of the Software.
.\"
.\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
.\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
.\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
.\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
.\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
.\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
.\" DEALINGS IN THE SOFTWARE.
.
.\" For code blocks and examples (cf groff's Ultrix-specific man macros)
.de EX
. in +\\$1
. nf
. ft CR
..
.de EE
. ft
. fi
. in
..
.
.SH SYNOPSIS
.PP
.B samtools tview
.RB [ -p
.IR chr:pos ]
.RB [ -s
.IR STR ]
.RB [ -d
.IR display ]
.I in.sorted.bam
.RI [ ref.fasta ]
.SH DESCRIPTION
.PP
Text alignment viewer (based on the ncurses library). In the viewer,
press `?' for help and press `g' to check the alignment start from a
region in the format like `chr10:10,000,000' or `=10,000,000' when
viewing the same reference sequence.
The top line shows the reference sequence, or '\fBN\fR's if unknown.
Underneath this is the consensus, derived from the sequence
alignments. Below the consensus the sequence alignment records are
shown. Uppercase and lowercase is used to distinguish the sequence
strand, with uppercase being the top/forward strand.
When the reference is known, both consensus and alignment record
sequences are displayed in a dot-notation where a matching character
is shown as '\fB.\fR' (forward strand) or '\fB,\fR' (reverse strand) and only
mismatching bases and missing bases are shown. This mode can be
toggled with the "." command.
.SH OPTIONS
.TP 14
.BI -d \ display
Output as (H)tml, (C)urses or (T)ext.
The width of generated text is controlled by the COLUMNS environment
variable or the \fB-w\fR option for non-curses outputs.
Note this may be a local shell variable so it may need
exporting first or specifying on the command line prior to the
command. For example
.EX 2
export COLUMNS ; samtools tview -d T -p 1:234567 in.bam
.EE
.TP
.BI -p \ chr:pos
Go directly to this position
.TP
.BI -s \ STR
Display only alignments from this sample or read group. \fBSTR\fR
must match either an \fBID\fR or \fBSM\fR field in an \fB@RG\fR header
record. For example
.EX 2
samtools tview -p chr20:10M -s NA12878 grch38.fa
.EE
.TP
.BI -w \ INT
Specifies the display width when using the HTML or Text output modes.
.TP
.B -X
If this option is set, it will allows user to specify customized index file location(s) if the data
folder does not contain any index file. Example usage: samtools tview [options] -X </data_folder/data.bam> [/index_folder/index.bai] [ref.fasta]
.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
|
