Main logo
?
tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

SAMtools

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.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community
Sort by:

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

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

SAMtools classification

SAMtools specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C, Perl
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
License:
BSD 2-clause “Simplified” License, MIT License
Stability:
Stable
Wikipedia:
https://en.wikipedia.org/wiki/SAMtools

Subtools

  • 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

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

download

SAMtools support

Maintainer

  • Heng Li <>

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

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.