Samtools at GitHub is an umbrella organisation encompassing several groups working on formats and tools for next-generation sequencing:

File-format specifications

The hts-specs repository contains the specifications of several sequence data formats (SAM, BAM, and CRAM), variant calling data formats (VCF and BCF), feature data formats (BED), and related formats such as indexing, encryption, and transfer protocols. Changes to these formats are discussed as issues and pull requests there.

C API and high-throughput sequencing tools

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.

Java API

The htsjdk repository contains a Java API for manipulating these formats. HTSJDK is used by the picard tools hosted elsewhere.

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.