Links in bold point to the corresponding PDFs on this repository's GitHub Pages website.
SAMv1.tex is the canonical specification for the SAM (Sequence Alignment/Map) format, BAM (its binary equivalent), and the BAI format for indexing BAM files. SAMtags.tex is a companion specification describing the predefined standard optional fields and tags found in SAM, BAM, and CRAM files. These formats are discussed on the samtools-devel mailing list.
CRAMv3.tex is the canonical specification for the CRAM format, while CRAMv2.1.tex describes its now-obsolete predecessor. Further details can be found at ENA's CRAM toolkit page. CRAM discussions can also be found on the samtools-devel mailing list.
The tabix.tex and CSIv1.tex quick references summarize more recent index formats: the tabix tool indexes generic textual genome position-sorted files, while CSI is htslib's successor to the BAI index format.
VCFv4.3.tex is the canonical specification for the Variant Call Format and its textual (VCF) and binary (BCF) encodings, while VCFv4.1.tex and VCFv4.2.tex describe their predecessors. These formats are discussed on the vcftools-spec mailing list.
BCFv1_qref.tex summarizes the obsolete BCF1 format historically produced by samtools. This format is no longer recommended for use, as it has been superseded by the more widely-implemented BCF2.
BCFv2_qref.tex is a quick reference describing just the layout of data within BCF2 files.