The SAMtools source code is hosted on Github. You can check out the latest development source code with:

git clone git://github.com/samtools/samtools.git
git clone git://github.com/samtools/bcftools.git
git clone git://github.com/samtools/htslib.git

Please note the source code in this repository is under development and make contain experimental or untested code. We recommend you do not use it in production pipelines unless specifically advised.