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/index.bai] [ref.fasta]

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1)

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