SAM/BAM and related specifications
These documents are maintained by the Large Scale Genomics work stream of the Global Alliance for Genomics & Health (GA4GH). Information on GA4GH procedures and how to get involved is available here. Lists of contributors and acknowledgements can generally be found in each individual specification document.
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. 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. CRAMcodecs.tex contains details of the CRAM custom compression codecs. Further details can be found at ENA’s CRAM toolkit page and GA4GH’s CRAM 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.
Unaligned sequence data files
We do not define or endorse any dedicated unaligned sequence data format. Instead we recommend storing such data in one of the alignment formats (SAM, BAM, or CRAM) with the unmapped flag set. However for completeness, we list the commonest formats below with external links.
FASTA is an early sequence-only format originally defined by William Pearson’s tool of the same name.
FASTQ was designed as a replacement for FASTA, combining the sequence and quality information in the same file. It has no formal definition and several incompatible variants, but is described in a paper by Cock et al.
Variant calling data files
VCFv4.5.tex is the canonical specification for the Variant Call Format and its textual (VCF) and binary (BCF) encodings, while VCFv4.1.tex, VCFv4.2.tex, VCFv4.3.tex and VCFv4.4.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 This format is no longer recommended for use, as it has been superseded by the more widely-implemented BCF2.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.
Discrete genomic feature data files
BEDv1.tex is the canonical specification for the GA4GH Browser Extensible Data (BED) format.
File encryption
crypt4gh.tex is the canonical specification of the crypt4gh format which can be used to wrap existing file formats in an encryption layer.
Transfer protocols
Htsget.md describes the hts-get retrieval protocol, which enables parallel streaming access to data sharded across multiple URLs or files.
Refget.md enables access to reference sequences using an identifier derived from the sequence itself.