HTS-spec GitHub page
SAMv1.pdf
CRAMv2.1.pdf
CRAMv3.pdf
BCFv1.pdf
BCFv2.1.pdf
CSIv1.pdf
tabix.pdf
VCFv4.1.pdf
VCFv4.2.pdf
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. 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.
VCFv4.1.tex and VCFv4.2.tex are the canonical specifications for the Variant Call Format and its textual (VCF) and binary encodings (BCF 2.x). 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 This format is no longer recommended for use, as it has been superseded by the more widely-implemented BCF2.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.