Twelve years of SAMtools and BCFtools

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 fir...

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Bibliographic Details
Published in:Gigascience 2021-02, Vol.10 (2)
Main Authors: Danecek, Petr, Bonfield, James K, Liddle, Jennifer, Marshall, John, Ohan, Valeriu, Pollard, Martin O, Whitwham, Andrew, Keane, Thomas, McCarthy, Shane A, Davies, Robert M, Li, Heng
Format: Article
Language:English
Subjects:
Genome
Genomics
High-Throughput Nucleotide Sequencing
Next-generation sequencing
Packages
Software
Source code
Statistical analysis
Statistical methods
Technical Note
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Summary: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.
ISSN:2047-217X
2047-217X
DOI:10.1093/gigascience/giab008