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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. Under- neath this is the consensus, derived from the sequence alignments. Be- low the consensus the sequence alignment records are shown. Uppercase and lowercase is used to distinguish the sequence strand, with upper- case being the top/forward strand. When the reference is known, both consensus and alignment record se- quences are displayed in a dot-notation where a matching character is shown as '.' (forward strand) or ',' (reverse strand) and only mis- matching 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 out- puts. 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/in- dex.bai] [ref.fasta] AUTHOR Written by Heng Li from the Sanger Institute. SEE ALSO samtools(1) Samtools website: <http://www.htslib.org/> samtools-1.21 12 September 2024 samtools-tview(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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