Decision support

Compare standards by the job they do

Place up to three profiles side by side. Focus on architectural role, evidence, and the first limitation to test—not on finding a single all-purpose standard.

Working set

Choose profiles

1 of 3 selected

SAM/BAM · CRAM · VCF/BCFStandard

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Decision lens

Compare roles before you compare maturity.

The useful question is not “Which standard wins?” It is “Which job must this part of the architecture perform, and what remains uncovered?”

Start with the job
Decide whether you need guidance, a domain payload, exchange, semantics, governance, or a reusable release.
Map lifecycle reach
Use the matrix to see where each profile has a direct role. A filled cell is coverage, not a quality score.
Test the boundary
Read what each option leaves unresolved before judging maturity, confidence, or implementation fit.

Three-part assessment

See the reach, the gaps, and the evidence.

Read left to right. Lifecycle reach comes first; maturity remains an editorial roll-up, not certification.

01 · Lifecycle reach

Where each profile contributes directly

Coverage shows a recorded role at that readiness stage. It does not imply end-to-end implementation.

Readiness-stage coverage for GA4GH HTS Format Specifications
Profile	Plan	Acquire	Harmonize	Exchange	Learn + reuse
SAM/BAM · CRAM · VCF/BCFStandard	GA4GH HTS Format Specifications has no direct role recorded in Plan.	GA4GH HTS Format Specifications has a direct role in Acquire.	GA4GH HTS Format Specifications has a direct role in Harmonize.	GA4GH HTS Format Specifications has a direct role in Exchange.	GA4GH HTS Format Specifications has a direct role in Learn + reuse.

Direct role recordedNo direct role recorded

02 · Boundaries

What each option does not cover

These are design boundaries, not faults. Use them to identify the companion layers your architecture still needs.

SAM/BAM · CRAM · VCF/BCF

Stage boundary: No direct role is recorded for Plan.
Known limitation: Format conformance does not establish sample identity, consent, reference correctness, variant normalization, QC, or pipeline reproducibility. FASTQ has no formal hts-specs definition.

03 · Detailed assessment

Check the fit and evidence behind the map

Use the source, status, and limitation together. A higher maturity label does not erase a scope mismatch.

Detailed comparison of GA4GH HTS Format Specifications
Assessment	SAM/BAM · CRAM · VCF/BCFGA4GH HTS Format Specifications
Purpose & coverage	Sequence alignments, compressed reference-oriented reads, variant calls, binary encodings, standard tags, and associated indexes. Best fitThe base interchange layer for sequencing alignments and variant-call datasets across pipelines, archives, and analysis tools.
Readiness stages	AcquireHarmonizeExchangeLearn + reuse
AI-ready contribution	Creates stable record-level inputs for genomic feature engineering, while phenotype linkage, cohort design, QC, and leakage controls remain external.
First limitation to test	Format conformance does not establish sample identity, consent, reference correctness, variant normalization, QC, or pipeline reproducibility. FASTQ has no formal hts-specs definition.
Evidence	E1 + E2 High confidence Formal statusCurrent canonical family; SAM/BAM 1.6, CRAM 3.1, VCF 4.5 / BCF 2.2 ReviewSource-checked
Maturity	Established Canonical genomic formats with long-standing multi-tool and repository use
Sources & links	GA4GH / Samtools HTS specifications (opens in a new tab)Read full profile