samtools tview

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

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.

-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]

Written by Heng Li from the Sanger Institute.

samtools(1)

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