Open Access

GigaScience

, volume 10 , issue 2

Twelve years of SAMtools and BCFtools

Petr Danecek ¹

James K Bonfield ¹

Jennifer Liddle ¹

John Marshall ²

Valeriu Ohan ¹

Martin O Pollard ¹

Andrew Whitwham ¹

Thomas Keane ³

Susan A. MaCarthy ¹

Robert M Davies ¹

Heng Li ^{4, 5}

Hide authors affiliations Show authors affiliations: 5 affiliations

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK |

Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1QH, UK |

EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK |

⁴

Department of Data Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA |

⁵

Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02215, USA |

Publication type: Journal Article

Publication date: 2021-01-29

Oxford University Press

GigaScience

scimago Q1

wos Q1

SJR: 5.314

CiteScore: 20.0

Impact factor: 3.9

ISSN: 2047217X

DOI: 10.1093/gigascience/giab008

Copy DOI

PubMed ID: 33590861

Computer Science Applications

Health Informatics

Abstract

Background

SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.

Findings

The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.

Conclusion

Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.

Found

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Gorodnichev Roman

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Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency

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Central Research Institute of Epidemiology of Rospotrebnadzor

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NGS

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Siberian Institute of Plant Physiology and Biochemistry of the Siberian Branch of the Russian Academy of Sciences

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Saint-Petersburg Pasteur Institute

Irkutsk State Medical University

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Wai Kar

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Yao Gang

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Kunming Institute of Botany, Chinese Academy of Sciences

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Linhua Sun

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Nanjing Normal University

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Morgante Verónica

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Haseloff Jim

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Danecek P. et al. Twelve years of SAMtools and BCFtools // GigaScience. 2021. Vol. 10. No. 2.

GOST all authors (up to 50) Copy

Danecek P., Bonfield J. K., Liddle J., Marshall J., Ohan V., Pollard M. O., Whitwham A., Keane T., MaCarthy S. A., Davies R. M., Li H. Twelve years of SAMtools and BCFtools // GigaScience. 2021. Vol. 10. No. 2.

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RIS Copy

TY - JOUR

DO - 10.1093/gigascience/giab008

UR - https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab008/6137722

TI - Twelve years of SAMtools and BCFtools

T2 - GigaScience

AU - Danecek, Petr

AU - Bonfield, James K

AU - Liddle, Jennifer

AU - Marshall, John

AU - Ohan, Valeriu

AU - Pollard, Martin O

AU - Whitwham, Andrew

AU - Keane, Thomas

AU - MaCarthy, Susan A.

AU - Davies, Robert M

AU - Li, Heng

PY - 2021

DA - 2021/01/29

PB - Oxford University Press

IS - 2

VL - 10

PMID - 33590861

SN - 2047-217X

ER -

BibTex

Cite this

BibTex (up to 50 authors) Copy

@article{2021_Danecek,

author = {Petr Danecek and James K Bonfield and Jennifer Liddle and John Marshall and Valeriu Ohan and Martin O Pollard and Andrew Whitwham and Thomas Keane and Susan A. MaCarthy and Robert M Davies and Heng Li},

title = {Twelve years of SAMtools and BCFtools},

journal = {GigaScience},

year = {2021},

volume = {10},

publisher = {Oxford University Press},

month = {jan},

url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab008/6137722},

number = {2},

doi = {10.1093/gigascience/giab008}

}

Publisher

Oxford University Press

Journal

GigaScience

scimago Q1

wos Q1

SJR

5.314

CiteScore

20.0

Impact factor

3.9

ISSN

2047217X (Electronic)

Profiles

Thomas M Keane