Command-line tool

samtools

brew/samtools

Checked 25 Oct 2026, 21:09 UTC · Listing refreshed from Homebrew, winget, npm, Scoop and cargo; npm packages checked against OSV.dev

Tools for manipulating next-generation sequencing data

Website

At a glance

Type

Command-line tool

Install on

macOS, Linux

Last checked

25 Oct 2026, 21:09 UTC

Install it

macOS

brew install samtools

Linux

brew install samtools

Convert a SAM input file to BAM stream and save to file

samtools view -S -b input.sam > output.bam

Take input from `stdin` (-) and print the SAM header and any reads overlapping a specific region to `stdout`

other_command | samtools view -h - chromosome:start-end

Sort file and save to BAM (the output format is automatically determined from the output file's extension)

samtools sort input -o output.bam

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