SAMtools protocols

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



Add your version


  • person_outline Heng Li <>

Publications for SAMtools

SAMtools IN pipelines

PMCID: 5755806
PMID: 29304111
DOI: 10.1371/journal.pone.0190670

[…] sequences were aligned and mapped onto the b73 reference genome ( using bwa software [18]. snp calling was performed using samtools software [18]. low-quality snps with a base quality value <20 and a read depth <4× the coverage from the gsh pool sequences were excluded. snp-index values [12,19] were calculated […]

PMCID: 5764945
PMID: 29326221
DOI: 10.1128/genomeA.01446-17

[…] (13). alignment to the reference genome of a. laidlawii pg-8a (genbank accession number cp000896) and annotation of single nucleotide polymorphisms (snps) were performed using bowtie2 software (14), samtools (15), and snpeff version 3.3 (16). gene prediction and annotation were performed using the ncbi prokaryotic genome annotation pipeline (17)., mutations in the genes associated […]

PMCID: 5773744
PMID: 29348359
DOI: 10.1128/genomeA.01507-17

[…] reads) (thermo fisher, usa) were mapped against the contig from the pacbio assembly using bowtie 2 version 2.2.4 (5). to spot possible frameshifts, single nucleotide variants were called using samtools version 1.3 (6), and the errors were corrected manually with the visual aid of geneious version 10.1.2 (7). the resulting full genome is 2,363,414 bp, with a gc content of 37.1% […]

PMCID: 5776139
PMID: 29386992
DOI: 10.3389/fnmol.2017.00429

[…] contained four libraries with different barcodes., raw reads were mapped on transcriptome of rat genome rnor 6.0 version by using bwa aligner (li et al., 2009). raw read counts were evaluated by samtools software (li et al., 2009). set of differentially expressed (de) genes were estimated by deseq2 (love et al., 2014)., list of genes that are selectively expressed in different cells types […]

PMCID: 5786212
PMID: 29340582
DOI: 10.1093/gbe/evx274

[…] from all pools against the final transcriptome assembly, using the k 1 parameter to report a single best hit for each read. following alignment, read counts for each transcript were generated using idxstats in samtools v.1.2, (li et al. 2009)., the edger package (robinson et al. 2010) was used to calculate significant differences in gene expression between infected and non-infected groups […]

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.