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 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.