01
Where it fits and where it does not
Use these four checks before committing implementation time.
- Use it when
- The base interchange layer for sequencing alignments and variant-call datasets across pipelines, archives, and analysis tools.
- Limits
- Format conformance does not establish sample identity, consent, reference correctness, variant normalization, QC, or pipeline reproducibility. FASTQ has no formal hts-specs definition.
- Best for
- Omics teams working across Acquire → Harmonize → Exchange → Learn + reuse.
- Maturity
- EstablishedSuitable for production assessment. Pin the exact release and any implementation profile.
02
See it in the workflow
This view shows the input, the change the standard introduces, and the resulting output.
- InputWhat starts
Omics source data, metadata, and local mappings
- SAM/BAM · CRAM · VCF/BCFWhat changes
Use SAM/BAM · CRAM · VCF/BCF as a pinned standard across Acquire → Harmonize → Exchange → Learn + reuse
- OutputWhat becomes possible
A handoff the next system or team can validate against the same release
03
A concrete example
A pipeline emits BAM or CRAM with a pinned reference checksum and validated headers, then emits normalized VCF 4.5 or BCF 2.2 with provenance, indexes, and checksums.
Why it matters: Creates stable record-level inputs for genomic feature engineering, while phenotype linkage, cohort design, QC, and leakage controls remain external.
04
What it fits with
Complements GA4GH DRS/WES: DRS locates objects, WES runs workflows, htsget streams these formats, and refget resolves reference sequences. ISA or MINSEQE carries study context.
- Metadata profileSDRF-Proteomics
Both support Omics work and meet around Acquire, Harmonize, Exchange, Learn + reuse. Compare their roles before treating them as interchangeable.
Explore relationship - Metadata vocabularyDPV
Both support Omics work and meet around Acquire, Harmonize, Exchange, Learn + reuse. Compare their roles before treating them as interchangeable.
Explore relationship - Data model / schemaPDBx/mmCIF
Both support Omics work and meet around Acquire, Harmonize, Exchange, Learn + reuse. Compare their roles before treating them as interchangeable.
Explore relationship - Data model / schemaAIRR · MiAIRR
Both support Omics work and meet around Acquire, Harmonize, Exchange, Learn + reuse. Compare their roles before treating them as interchangeable.
Explore relationship
05
Implementation starter
Start with one bounded handoff. Pin, test, and review it before scaling.
Define one handoff, its accountable owner, and the decision SAM/BAM · CRAM · VCF/BCF must support.
Pin the exact version and companion artifacts: SAM/BAM 1.6 · CRAM 3.1 · VCF 4.5 / BCF 2.2.
Map one representative input to the required standard artifacts.
Test the result against the canonical source and record every exception.
Preserve the source data, mappings, and review evidence before scaling.
06
Test the main limitation
Format conformance does not establish sample identity, consent, reference correctness, variant normalization, QC, or pipeline reproducibility. FASTQ has no formal hts-specs definition.
Run one representative end-to-end pilot and record exactly where SAM/BAM · CRAM · VCF/BCF loses context, needs an extension, or depends on another standard.
Machine-readable output may still be unfit for analysis or ML.
Test the output for missing context, provenance, terminology alignment, time leakage, and the intended downstream decision. Creates stable record-level inputs for genomic feature engineering, while phenotype linkage, cohort design, QC, and leakage controls remain external.
07
Official resources
Specifications, diagrams, examples, and guides from the organizations that maintain them.
GA4GH / Samtools HTS specifications
Official publisher or steward guidance for this standard profile.
- Publisher
- GA4GH Large Scale Genomics work stream · Samtools specification community