SAMtools / BCFtools / HTSlib

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

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.

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.

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 Martin O. Pollard

Martin O. Pollard

Technical Innovator

Photo of Robert Davies

Robert Davies

Senior Scientific Manager

Photo of Dr Shane A. McCarthy

Dr Shane A. McCarthy

Senior Scientific Manager

Previous contributors

Photo of John Marshall

John Marshall

Senior Software Developer

Photo of Dr Joshua C. Randall

Dr Joshua C. Randall

Senior Scientific Manager

External Contributors