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

NAME
       samtools	 tview	-  display  alignments	in  a curses-based interactive
       viewer.

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

DESCRIPTION
       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.

OPTIONS
       -d display    Output as (H)tml, (C)urses	or (T)ext.

		     The width of generated text is controlled by the  COLUMNS
		     environment  variable.   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

		       export COLUMNS ;	samtools tview -d T -p 1:234567	in.bam

       -p chr:pos    Go	directly to this position

       -s STR	     Display only alignments from this sample or read group

       -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/in-
		     dex.bai] [ref.fasta]

AUTHOR
       Written by Heng Li from the Sanger Institute.

SEE ALSO
       samtools(1)

       Samtools	website: <http://www.htslib.org/>

samtools-1.11		       22 September 2020	     samtools-tview(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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