samtools-tview - display alignments in a curses-based interactive viewer.
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/>