Aver CLI¶
Know whether your pipeline is still validated after every change.
The Aver CLI fingerprints a bioinformatics pipeline's dependencies, runs it on public Genome in a Bottle (GIAB) reference reads, and measures its SNV and indel performance with hap.py and the RTG vcfeval engine. It writes a deterministic, verifiable report you can file.
- Local and free. No account, and no network calls other than downloading reference data, the pipeline and its containers. No telemetry.
- Public reference materials only. Aver benchmarks against GIAB samples (HG001–HG007) for germline and the SEQC2 HCC1395/HCC1395BL cell-line pair for somatic. It has no field anywhere for a patient identifier or a clinical sample, and it refuses any VCF whose sample is not a registered reference material.
- Reproducible. Reference data is verified against recorded SHA-256 checksums, containers are pinned by digest, and the same inputs always produce the same snapshot hash and byte-identical report.
Newer capabilities, documented on their own pages:
- Run QC monitoring — push each run's metrics (numbers only) and trend them against control limits your laboratory sets; rule-derived flags, audited dispositions.
- DRAGEN pipelines — snapshot a vendor configuration from the replay file each run already writes, so a DRAGEN upgrade shows up as drift like any other change.
- Somatic pipelines — per-class recall and precision against the SEQC2 high-confidence calls, with the truth-set version and checksums recorded on every run.
- Structural variants — SVs ≥50bp benchmarked with truvari against the GIAB HG002 Tier 1 truth set, exactly as its README recommends.
- Pharmacogenomics — star-allele diplotype calls judged gene by gene against the CDC GeT-RM published consensus for 363 public Coriell samples.
New to pipeline validation? Start with the guides: benchmarking against GIAB, what pipeline drift is and revalidating after a tool upgrade.
Run QC results also land in your evidence packs: the window's runs, limit versions and every flag with its disposition, in the same signed, verifiable document.
Aver produces validation evidence. It does not certify, accredit or approve anything. Determinations about the fitness of a pipeline for clinical use remain the responsibility of the laboratory and its accrediting body.