Tool
Analysis
Annotation
Data formats
Sequence data processing

SAMtools / BCFtools / HTSlib

SAMtools, BCFtools. and HTSlib are tools for manipulating sequence alignment (SAM, BAM, CRAM) and variant call (VCF and BCF) files.

SAMtools, BCFtools and HTSlib packages
HTSlib is a software library for manipulating various sequencing and variant file formats: SAM, BAM, CRAM, VCF, and BCF. SAMtools and BCFtools are applications built around HTSlib, performing format conversion, file merging and splitting, sorting, variant calling, and much more.

About

For a full overview of the package see www.htslib.org for documentation and downloads. Code development is tracked at github.com/samtools in the appropriate sub-packages.

Downloads

Please download release tarballs from www.htslib.org.

SAMtools, BCFtools and HTSlib packages Download

Further information

All the code is non-encumbered OpenSource license, predominantly MIT with some BSD. Please see the top of each file for the specifics.

Contact

If you need help or have any queries, please contact us using the details below.

For bug reports or to ask questions, please use GitHub Issues for the appropriate repository:

Sanger Institute Contributors

Photo of James Bonfield

James Bonfield

Principal Software Developer

Photo of Dr Petr Danecek

Dr Petr Danecek

Statistical Genetics Analyst

Photo of Robert Davies

Robert Davies

Senior Scientific Manager

Photo of Mr Martin O. Pollard

Mr Martin O. Pollard

Technical Innovator

Photo of Andrew Whitwham

Andrew Whitwham

Senior Software Developer

Previous contributors

Photo of John Marshall

John Marshall

Senior Software Developer

Photo of Valeriu Ohan

Valeriu Ohan

Senior Software Developer

Photo of Dr Joshua C. Randall

Dr Joshua C. Randall

Senior Scientific Manager

External Contributor

Photo of Heng Li

Heng Li

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Publications

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