← Diligence index  ·  View raw .md  ·  Machine-readable JSON

Repeatability Proof — HG002 30× — 2026-05-12

Two independent runs of the locked Parabricks DeepVariant-germline pipeline on the same HG002 30× FASTQ input, on the same NVIDIA GB10 hardware. The purpose: confirm that "same input → same output" holds at the granularity clinical-lab QMS reviewers care about (variant calls), not the granularity that's bioinformatics noise (BAM/VCF metadata bytes).

Result

Field Value
Variant calls — run 1 7,593,649
Variant calls — run 2 7,593,649
Variant count delta 0
Variant-content SHA-256 (sorted, headers stripped) 713ac282be16ebf768a37f670727bc429a0c23adef1e6076c9cb60a04b7502d5 (both runs)
Variant-content byte-identical YES
Raw BAM byte-identical No (see "Why raw bytes differ" below)
Raw VCF byte-identical No (same reason)

Why raw BAM / VCF bytes differ but variants don't

Parabricks embeds two run-specific bytes into the BAM/VCF @PG (Program) header:

  1. The output filename passed via --out-bam / --out-variants (HG002.30x.bam vs HG002.30x.rerun.bam here)
  2. Implicit run timestamp metadata

These bytes are part of the @PG line in the BAM header and the ## header of the VCF. They are explicitly not part of the alignment records or the variant-call records. Strip the metadata headers (grep -v '^##'), sort the records (sort), SHA-256 the result, and both runs produce 713ac282…7502d5.

Run metadata

Run 1 Run 2
Image digest sha256:5bc63974…086f5287e2b sha256:5bc63974…086f5287e2b
Hardware NVIDIA GB10 (Grace ARM) NVIDIA GB10 (Grace ARM)
Start time (UTC) 2026-05-10T20:06:17Z 2026-05-12T14:52:18Z
Wall clock 1h 52m 13s (6,733s) 2h 7m 3s (7,623s)
Output BAM SHA-256 b519ac83…68c7396 c9eb3209…f0ef1978
Output VCF SHA-256 4fb4c416…3a726dc5f a0504b79…22b51bb
Variant count 7,593,649 7,593,649

The ~13% wall-clock difference between runs is normal — GPU thermal state and host-side I/O scheduler can shift run times by ~10–20% between otherwise-identical executions. Per-variant content is unaffected.

Why this is the claim that matters

A CLIA-CAP QMS reviewer assessing a secondary-analysis vendor cares about exactly one question: given the same input, does the pipeline always emit the same variant calls? The answer here is yes, bit-for-bit, across two independent runs.

Vendors who claim "byte-identical BAM/VCF files" are either (a) running on single-threaded software that emits headers deterministically, or (b) not running with metadata embedded in the file. Datamade Genomics runs multi-threaded GPU-accelerated Parabricks with full provenance metadata embedded in every artifact, and the biological content is still byte-identical across runs.

How to reproduce

# Requires the showcase HG002 30x FASTQs at /data/jobs/showcase-hg002-30x/input/
./scripts/run_repeatability_proof.sh
# Emits /data/jobs/showcase-hg002-30x/repeatability_report.json
# Expected: result.variant_content_identical == "yes"

Full machine-readable proof: repeatability_report.json