Twelve years of SAMtools and BCFtools

Petr Danecek; James K Bonfield; Jennifer Liddle; John Marshall; Valeriu Ohan; Martin O Pollard; Andrew Whitwham; Thomas Keane; Shane A McCarthy; Robert M Davies; Heng Li

doi:10.1093/gigascience/giab008

Twelve years of SAMtools and BCFtools

Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008.

Authors

Affiliations

¹ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
² Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1QH, UK.
³ 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.

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.

Keywords: bcftools; data analysis; high-throughput sequencing; next generation sequencing; samtools; variant calling.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome
Genomics
High-Throughput Nucleotide Sequencing*
Software*

Grants and funding

206194/WT_/Wellcome Trust/United Kingdom