Tools (written in C using htslib) for manipulating next-generation sequencing data
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bam_addrprg.c Improved multi-threading support for many more samtools commands. Feb 9, 2017
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sam.c Various tidying up and segfault fixes Apr 14, 2016
sam.h Add sam_index_load() and samfetch() to legacy API Mar 9, 2015
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sam_opts.h Improved multi-threading support for many more samtools commands. Feb 9, 2017
sam_utils.c Avoid printing "error message: Success" [minor] Jun 2, 2016
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README.md

samtools

This is the official development repository for samtools.

The original samtools package has been split into three separate but tightly coordinated projects:

  • htslib: C-library for handling high-throughput sequencing data
  • samtools: mpileup and other tools for handling SAM, BAM, CRAM
  • bcftools: calling and other tools for handling VCF, BCF

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

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 an extra step:

autoconf -Wno-syntax  # Generate the configure script, if needed
./configure           # Optional, 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.