SAMtools / BCFtools / HTSlib

SAMtools / BCFtools / HTSlib

SAMtools / BCFtools / HTSlib


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 for documentation and downloads. Code development is tracked at in the appropriate sub-packages.

Download and Installation

Please download release tarballs from

License and Citation

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


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


Sanger Contributors
External Contributors


  • The Sequence Alignment/Map format and SAMtools.

    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al.

    Bioinformatics (Oxford, England) 2009;25;16;2078-9

  • The variant call format and VCFtools.

    Danecek P, Auton A, Abecasis G, Albers CA, Banks E et al.

    Bioinformatics (Oxford, England) 2011;27;15;2156-8

  • Efficient storage of high throughput DNA sequencing data using reference-based compression.

    Hsi-Yang Fritz M, Leinonen R, Cochrane G and Birney E

    Genome research 2011;21;5;734-40

  • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

    Li H

    Bioinformatics (Oxford, England) 2011;27;21;2987-93

  • BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.

    Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C and Durbin R

    Bioinformatics (Oxford, England) 2016;32;11;1749-51

  • A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

    Danecek P, McCarthy SA, HipSci Consortium and Durbin R

    PloS one 2016;11;5;e0155014

  • Improving SNP discovery by base alignment quality.

    Li H

    Bioinformatics (Oxford, England) 2011;27;8;1157-8