1samtools-tview(1)            Bioinformatics tools            samtools-tview(1)
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NAME

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

10       samtools  tview  [-p  chr:pos]  [-s  STR]  [-d  display]  in.sorted.bam
11       [ref.fasta]
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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.
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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
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28                       export COLUMNS ; samtools tview -d T -p 1:234567 in.bam
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31       -p chr:pos    Go directly to this position
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33       -s STR        Display only alignments from this sample or read group
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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]
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AUTHOR

43       Written by Heng Li from the Sanger Institute.
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45

SEE ALSO

47       samtools(1)
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49       Samtools website: <http://www.htslib.org/>
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53samtools-1.13                     7 July 2021                samtools-tview(1)