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samtools

This is not the official development repository for samtools.

This is our version of samtools, based on the original version, on which we have added an interactive BAM viewer tool (accessible with the following command: samtools ADVIEW).

The official repository is here:

  • samtools: mpileup and other tools for handling SAM, BAM, CRAM

To build this tool, you will need to checkout the htslib project as ../htslib

The htslib can be found here:

  • htslib: C-library for handling high-throughput sequencing data

See also http://github.com/samtools/

This is not the official development repository for samtools.

This is our version of samtools, based on the original version, on which we have added an interactive BAM viewer tool.

The official repository is here:

  • samtools: mpileup and other tools for handling SAM, BAM, CRAM

To build this tool, you will need to checkout the htslib project as ../htslib

The htslib can be found here:

  • htslib: C-library for handling high-throughput sequencing data

See also http://github.com/samtools/

Build Status Build status Github All Releases

Building Samtools

See INSTALL for complete details. Release tarballs contain generated files that have not been committed to this repository, so building the code from a Git repository requires extra steps:

autoheader            # Build config.h.in (this may generate a warning about
                      # AC_CONFIG_SUBDIRS - please ignore it).
autoconf -Wno-syntax  # Generate the configure script
./configure           # Needed for choosing optional functionality
make
make install

By default, this will build against an HTSlib source tree in ../htslib. You can alter this to a source tree elsewhere or to a previously-installed HTSlib by configuring with --with-htslib=DIR.

Citing

Please cite this paper when using SAMtools for your publications.

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
GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008

@article{10.1093/gigascience/giab008,
    author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},
    title = "{Twelve years of SAMtools and BCFtools}",
    journal = {GigaScience},
    volume = {10},
    number = {2},
    year = {2021},
    month = {02},
    abstract = "{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.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.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.}",
    issn = {2047-217X},
    doi = {10.1093/gigascience/giab008},
    url = {https://doi.org/10.1093/gigascience/giab008},
    note = {giab008},
    eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab008/36332246/giab008.pdf},
}