SAM/BAM and related specifications
Alignment data files
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.
The CRAM format is described at ENA's CRAM toolkit page.
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.
Variant calling data files
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).
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 This format is no longer recommended for use, as it has been superseded by the more widely-implemented BCF2.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.