Samtools at GitHub is an umbrella organisation encompassing several groups working on formats and tools for next-generation sequencing:
The hts-specs repository contains the specifications of several sequence data formats (SAM, BAM, and CRAM), variant calling data formats (VCF and BCF), and related formats such as indices. Changes to these formats are discussed as issues and pull requests there.
The htslib repository contains a C API and library for manipulating these formats. The bcftools and samtools repositories contain C programs for manipulating these formats on the command line and for performing variant calling.
There are also several other historical repositories within the samtools organisation containing tools and source code that have since been integrated into htslib or that have been deprecated and remain available mainly for their historical interest.