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.
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
Go directly to this position
Display only alignments from this sample or read group
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 website: <http://www.htslib.org/>
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