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Twelve years of SAMtools and BCFtools

Petr Danecek; James Bonfield; Jennifer Liddle; John Marshall; Valeriu Ohan; Martin Pollard; Andrew Whitwham; Thomas Keane · GigaScience · 2021

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Author / responsible party
Petr Danecek; James Bonfield; Jennifer Liddle; John Marshall; Valeriu Ohan; Martin Pollard; Andrew Whitwham; Thomas Keane
Publisher
GigaScience
Year
2021
Language
English

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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.

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APA 7

Danecek, P, Bonfield, J, Liddle, J, Marshall, J, Ohan, V, Pollard, M, Whitwham, A, & Keane, T. (2021). Twelve years of SAMtools and BCFtools. https://doi.org/10.1093/gigascience/giab008

MLA

Danecek, Petr, et al. "Twelve years of SAMtools and BCFtools." 2021. https://doi.org/10.1093/gigascience/giab008.

Chicago

Danecek, Petr, James Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, and Thomas Keane. 2021. "Twelve years of SAMtools and BCFtools.". https://doi.org/10.1093/gigascience/giab008.

Harvard

Danecek, P. et al. 2021, Twelve years of SAMtools and BCFtools, GigaScience, available at: https://doi.org/10.1093/gigascience/giab008 [Accessed 8 Aug. 2026].

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Title
Twelve years of SAMtools and BCFtools
Author / contributors
Petr Danecek; James Bonfield; Jennifer Liddle; John Marshall; Valeriu Ohan; Martin Pollard; Andrew Whitwham; Thomas Keane
Publisher
GigaScience
Publication year
2021
Language
English

Subjects

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Documentation; Computer science; Software; Sorting; File format; World Wide Web; Data science; Database; Programming language
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