NAME

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

SYNOPSIS

       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/>

samtools-1.13                                      7 July 2021                                 samtools-tview(1)