1samtools-tview(1)            Bioinformatics tools            samtools-tview(1)
2
3
4

NAME

6       samtools  tview  -  display  alignments  in  a curses-based interactive
7       viewer.
8

SYNOPSIS

10       samtools  tview  [-p  chr:pos]  [-s  STR]  [-d  display]  in.sorted.bam
11       [ref.fasta]
12

DESCRIPTION

14       Text  alignment  viewer  (based on the ncurses library). In the viewer,
15       press `?' for help and press `g' to check the alignment  start  from  a
16       region  in  the  format  like  `chr10:10,000,000' or `=10,000,000' when
17       viewing the same reference sequence.
18
19

OPTIONS

21       -d display    Output as (H)tml, (C)urses or (T)ext.
22
23                     The width of generated text is controlled by the  COLUMNS
24                     environment  variable.   Note  this  may be a local shell
25                     variable so it may need exporting first or specifying  on
26                     the command line prior to the command.  For example
27
28                       export COLUMNS ; samtools tview -d T -p 1:234567 in.bam
29
30
31       -p chr:pos    Go directly to this position
32
33       -s STR        Display only alignments from this sample or read group
34
35       -X            If  this  option  is  set, it will allows user to specify
36                     customized index file location(s) if the data folder does
37                     not contain any index file. Example usage: samtools tview
38                     [options] -X  </data_folder/data.bam>  [/index_folder/in‐
39                     dex.bai] [ref.fasta]
40
41

AUTHOR

43       Written by Heng Li from the Sanger Institute.
44
45

SEE ALSO

47       samtools(1)
48
49       Samtools website: <http://www.htslib.org/>
50
51
52
53samtools-1.15.1                  7 April 2022                samtools-tview(1)
Impressum