SAMtools specifications


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


  • 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



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  • person_outline Heng Li <>

SAMtools articles

SAMtools citations

PMCID: 5932188

[…] the hiseq x ten sequencing system. reads were aligned to reference genome by burrows-wheeler aligner (li and durbin, 2009). sam alignment files were converted to bam format, sorted, and indexed with samtools (li and durbin, 2009) and then visualized by integrative genomics viewer (igv) (thorvaldsdóttir et al., 2013)., for conidiation assays, one mycelial plugs (9 mm in diameter) of each strain, […]

PMCID: 5917017

[…] mixed linear model (mlm; p + g + q + k) and simple model. kinship was observed in all these snps. the significant association threshold was 1/n, where n is the total number of snps and indels. samtools was used for manual verification of regions with significant association from the aligned resequencing reads against the am560 genome (obtained from jgi)., based on the snp annotation and ld […]

PMCID: 5894988

[…] were generated, with mean coverage of 60 to 96x. the bwa alignment algorithm was used to map sequence reads to the ucsc human genome reference build 19 [12]. snvs were detected using bcftools and samtools mpileup with disabled baq computation [13] and indels were detected with pindel [14] and annotated to dbsnp144 by annovar [15]. variants altering the coding sequence were selected […]

PMCID: 5894961

[…] multi-vision software package [13]. snvs were called by soapsnp [14] and small indels (<20bp) were identified using the samtools (tools for alignments in the sam format) version: 0.1.18,, the screening method of copy number variations (cnv) we use was previously described by wei xm et al. [15]. the cut-off value was built on the precondition that suggests […]

PMCID: 5880904

[…] for the identification of amr determinants, the ‘genefinder’ algorithm was employed, which maps the sequencing reads to a set of reference sequences using bowtie 2 followed by generation of an mpileup file using samtools (langmead and salzberg, 2012). to establish the presence of the reference sequence or nucleotide variations within the read set, a positive match had to meet the following […]

SAMtools institution(s)
Medical Population Genetics Program, Broad Institute, Cambridge Center, Cambridge, MA, USA

SAMtools reviews

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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

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