SAMtools statistics

Tool stats & trends

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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 2. […]


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 represe […]


Genomic alterations of ground glass nodular lung adenocarcinoma

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

[…] 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 on the […]


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

[…] using the accession numbers in Supplementary Fig.  and B, aligned to the reference genome hg19 for HCT116 cells and mm8 for mouse liver using Bowtie2, and filtered according to alignment scores using SAMtools. SRA files were converted to FASTQ format using the command fastq-dump in the SRA Toolkit ( before the alignment. Peaks were called using MACS2 without the – […]


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

[…] uality trimmed using FastQC (v0.11.5) and mapped to the mouse genome (mm9) using Bismark (v0.16.3) using the following options: “–bam –chunkmbs 1024 –multicore 8”. Mapped BAM files were sorted with SAMtools (v0.1.19-96b5f2294a) and methylation calls were extracted using the “Rsamtools” (v.1.22.0) and “data.table” (v.1.9.6) packages, as well as custom R scripts as previously described. Coverage w […]


Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

PMCID: 5952643
PMID: 29764441
DOI: 10.1186/s12902-018-0257-z
call_split See protocol

[…] and InDels was done using GATK Unified Genotyper, which uses a Bayesian genotype likelihood model to report alleles and Phred-scaled confidence values []. Variants (SNVs and indels) were called with SAMTools, with reference to public databases including dbSNP and 1000Genomes and gnomAD []. Analysis was performed with preference to variants located in genes implicated in atypical non-autoimmune fo […]


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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.