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.

       The  top  line  shows  the reference sequence, or 'N's if unknown.  Underneath this is the
       consensus, derived from  the  sequence  alignments.   Below  the  consensus  the  sequence
       alignment  records are shown.  Uppercase and lowercase is used to distinguish the sequence
       strand, with uppercase being the top/forward strand.

       When the reference is known, both consensus and alignment record sequences  are  displayed
       in  a  dot-notation  where  a  matching character is shown as '.'  (forward strand) or ','
       (reverse strand) and only mismatching bases and missing bases are shown.  This mode can be
       toggled with the "."  command.

OPTIONS

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

                     The  width  of  generated  text  is  controlled  by  the COLUMNS environment
                     variable or the -w option for non-curses outputs.  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.   STR  must  match
                     either an ID or SM field in an @RG header record.  For example

                       samtools tview -p chr20:10M -s NA12878 grch38.fa

       -w INT        Specifies the display width when using the HTML or Text output modes.

       -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/>