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samtools-tview(1) Bioinformatics tools samtools-tview(1) 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 lower- case 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 en- vironment variable or the -w option for non-curses outputs. Note this may be a local shell variable so it may need ex- porting 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 out- put modes. -X If this option is set, it will allows user to specify cus- tomized index file location(s) if the data folder does not contain any index file. Example usage: samtools tview [op- tions] -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-1.23.1 18 March 2026 samtools-tview(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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