Tools (written in C using htslib) for manipulating next-generation sequencing data
Tools (written in C using htslib) for manipulating next-generation sequencing data
This is the official development repository for samtools.
The original samtools package has been split into three separate but tightly coordinated projects:
See also http://github.com/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 installBy 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.
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
…If you have found a bug or would like a new feature, please report the same in the GitHub SAMtools issue tracker.
For any security related issue, please send a mail to [email protected] instead of reporting in the GitHub issue tracker.
No open issues yet, or sync has not completed.