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Twelve years of SAMtools and BCFtools

Petr DanecekWellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SA,James BonfieldWellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SA,Jennifer LiddleWellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SA,John MarshallWolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow , Switchback Road, Glasgow, G61 1QH,Valeriu OhanWellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SA,Martin PollardWellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SA,Andrew WhitwhamWellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SA,Thomas KeaneEMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire , CB10 1SD,Shane McCarthyWellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SA,Robert M. DaviesWellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SA,Heng LiDepartment of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street , Boston, MA 02215,

2021en

ABI

Annotatsiya

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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DOI: 10.1093/gigascience/giab008

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