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A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. SAMtools can also index reference sequence in the FASTA format or extract subsequence from indexed reference sequence.

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4 user reviews

4 user reviews

Emeric Dynomant's avatar image Emeric Dynomant's country flag

Emeric Dynomant

THE soft to use with .bam / .sam ! Huge community and exemples availables !

Joseale Romero's avatar image Joseale Romero's country flag

Joseale Romero

Indispensable to work with BAM/SAM alignment files. Sorts, indexes, views...

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

Indispensable when you work with .bam files or .sam ! This is THE tool to manipulate these files !

Claudia Armenise Quartz Bio's avatar image

Claudia Armenise Quartz Bio

The most useful tool to deal with SAM and BAM files... There is a R Bioconductor package interfacing most of the tools (indexing, conversion...)

SAMtools forum

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SAMtools classification

SAMtools specifications

Software type:
Restrictions to use:
Programming languages:
C, Perl
Computer skills:
Command line interface
Operating system:
BSD 2-clause “Simplified” License, MIT License


  • view
  • sort
  • index
  • idxstats
  • flagstat
  • stats
  • bedcov
  • depth
  • merge
  • faidx
  • tview
  • split
  • quickcheck
  • dict
  • fixmate
  • mpileup
  • flags
  • fastq
  • fasta
  • collate
  • reheader
  • cat
  • rmdup
  • addreplacerg
  • calmd
  • targetcut
  • phase
  • depad

SAMtools distribution


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SAMtools support


  • Heng Li <>


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Medical Population Genetics Program, Broad Institute,Cambridge, MA, USA

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.