SAMtools protocols

View SAMtools computational protocol

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

Associated diseases

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



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  • person_outline Heng Li <>

Publications for SAMtools

SAMtools in pipelines

PMCID: 5754119
PMID: 29300782
DOI: 10.1371/journal.ppat.1006750

[…] []. duplicates were removed based on 5’ and 3’ positions ( reads shorter than 30 base pairs and with mapping quality less than 30 were removed using samtools []. the resulting bam files were processed using mapdamage 2.0 on default settings with plotting and statistical estimation []. haplogrep v2.1.0 [] using phylotree build 17 [] was used […]

PMCID: 5755140
PMID: 29301499
DOI: 10.1186/s12885-017-3943-8

[…] []. additionally, the initial 5 bases were trimmed due to potential allele bias in case of single nucleotide polymorphisms (snp) present in restriction enzyme cutting sites. snps were called with samtools mpileup algorithm with default parameters []. coverage cutoff value was 20., distribution of snps in examined nmsc population was compared to the european population (data derived […]

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

[…] sequences were aligned and mapped onto the b73 reference genome ( using bwa software []. snp calling was performed using samtools software []. 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 [,] were calculated […]

PMCID: 5755908
PMID: 29304067
DOI: 10.1371/journal.pone.0190685

[…] ( reads were aligned to the s. cerevisiae genome r64 using hisat 2.0.3-beta []. non-uniquely mapping reads (mapq < 10) were filtered out using samtools 1.3.1 []. analysis of differential gene expression was performed using r 3.2.3 ( and the bioconductor package deseq2 [,] at a 5% false discovery rate. significance […]

PMCID: 5756397
PMID: 29304727
DOI: 10.1186/s12864-017-4416-9

[…] resequenced with 20x target coverage. the sequence reads were aligned to the chicken reference genome (galgal4) [] using burrows-wheeler alignment algorithm implemented in bwa [] and sorted using samtools []. picard tools were used to mark duplicates and gatk was used for calling the snps [, ]. for more details on the preparation pipeline see reimer et al. []., the initial array data set […]

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SAMtools in publications

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 […]

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 […]

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 […]

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 […]

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 […]

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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.