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Popular tool citations

chevron_left SNP detection SNV detection File indexation Known transcript quantification File format conversion File merging Duplicate read removal File filtering Indel detection File sampling Tag count Variant detection Variant detection Depth of coverage File splitting File sorting chevron_right

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Associated diseases
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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


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




No version available


  • person_outline Heng Li

Publications for SAMtools

SAMtools citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] prinseq-lite (version 0.20.4). resulting high-quality reads were simultaneously mapped against the mus musculus (grcm38) and drosophila melanogaster (dm6) reference genomes via bwa (version 0.7.15). samtools (version 1.4) was used to split the alignments into mouse and drosophila reads. read normalization via the drosophila melanogaster spike-in material was carried out with deeptools (version […]


Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double strand breaks

Nat Commun
PMCID: 5959919
PMID: 29777105
DOI: 10.1038/s41467-018-04256-y

[…] of the chromosome was derived from both s799 and yph499, the mutation was annotated as a bir, and rearranged positions were further searched from the chimera sequences around the events using blast, samtools (, and perl/shell scripts. partial chimeric sequences from the pair within a chromosome were annotated as sgcs. because homologous tls, birs, and sgcs […]


Cattle with a precise, zygote mediated deletion safely eliminate the major milk allergen beta lactoglobulin

Sci Rep
PMCID: 5955954
PMID: 29769555
DOI: 10.1038/s41598-018-25654-8

[…] the reads were trimmed and joined as before and mapped to the target region of the bovine genome using bwa version 0.7.9a-r786 with default settings. mutations were enumerated using the functions in samtools version 1.1., all samples were assayed according to the method detailed in the bio-rad droplet digital™ pcr applications guide. briefly, ddpcr reactions were prepared to a final […]


Genomic alterations of ground glass nodular lung adenocarcinoma

Sci Rep
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] pe cluster kit and truseq rapid sbs kit (illumina)., sequence reads were mapped to the human genome (hg19) using burrows-wheeler alignment tool. duplicate read removal was performed using picard and samtools, and local alignment was optimized by the genome analysis toolkit. variant calling was only performed in targeted regions of cancerscan. somatic variant calling of each tumor was based […]


Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

Nat Commun
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] following analyses. replicate 1 for high methionine condition was not used due to abnormally high fraction of drosophila-originated reads in this sample. processing of alignment files was done using samtools. peaks were called using the --broad mode of macs2 and filtered with the criterion that enrichment q-value is smaller than 10−5. for mouse liver, chip-seq reads were aligned to the mouse […]


B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

Nat Commun
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] trimmed fastq files were mapped to the mouse genome (mm9) using tophat (v2.1.1) with the following settings: “-p 10 -n 2 --max-multihits 1 --read-gap-length 1”. mapped bam files were sorted with samtools (v0.1.19-96b5f2294a). gene-level expression of ucsc knowngenes were determined by calculating the number of reads that uniquely overlap gene exons using r/bioconductor (v.3.2.3) […]

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

SAMtools reviews

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Sangram keshari sahu

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One tool to handle most of the tasks related to Alignment files (SAM, BAM, CRAM). That may be indexing, statistics (like coverage and depth), editing and viewing the alignment data in the terminal. It also helps in file conversion from one alignment file format to another.

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.