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.