We have validated our variant-calling pipeline against the certified reference material NIST GIAB HG002 (GRCh38 v4.2.1), evaluating the metrics with hap.py following GA4GH standards.
The results, under the PASS filter, reach an F1 of 97.9% on SNVs and an F1 of 90.3% on INDELs, with full traceability: pinned versions, a documented callable region, and discordance analysis included.
Why it matters
Beyond producing a VCF, our goal is to deliver clinically defensible analyses. Validation against certified reference material ensures every project starts from a reproducible, auditable baseline.