SAMtools specifications

Unique identifier:
OMICS_00090
Interface:
Command line interface
Input format:
SAM, BAM, CRAM
Operating system:
Unix/Linux
License:
BSD 2-clause “Simplified” License, MIT License
Stability:
Stable
Wikipedia:
https://en.wikipedia.org/wiki/SAMtools
Software type:
Package/Module
Restrictions to use:
None
Output format:
SAM, BAM, CRAM, VCF
Programming languages:
C, Perl
Computer skills:
Advanced
Maintained:
Yes

Subtools

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

versioning

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No versioning.

SAMtools distribution

download

SAMtools support

Maintainer

  • Heng Li <>

forum

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Credits

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Publications

Institution(s)

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

User review

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5 user reviews

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5 user reviews

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Arup Ghosh's avatar image Arup Ghosh's country flag

Arup Ghosh

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From sam/bam conversion to variant calling Samtools have a large number of options for exploring aligned sequence files.

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

Emeric Dynomant

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

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

Joseale Romero

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

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

Fabien Pichon

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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

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

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