Tertiary Pipelines

Tertiary pipelines take a VCF — usually produced upstream by a secondary pipeline — and produce annotated, classified, report-ready variants. Each clinical reporter is its own tertiary pipeline.

Inputs

• VCF — the output of a secondary run (or an externally-provided VCF that meets the requirements).
• Sample metadata — tumor type, suspected phenotype, family history, depending on the reporter.
• Common inputs shared across reporters — see Common Inputs.

Outputs

• Annotated VCF with per-variant pathogenicity, ACMG criteria (for hereditary) or AMP/ASCO/CAP tier (for somatic), gene-level annotations, population frequencies.
• A report-ready dataset that the Report entity can render into a clinical PDF.

Reporters available

• GS Hereditary Reporter
• GS Hereditary Cancer Reporter
• GS Somatic Reporter
• GS Myeloid Reporter
• GS PGX Reporter

See also

• Common Inputs — reference genome, BED files, gene panels.
• Requirements — minimum metadata and QC thresholds.
• Variant Filtering — how the outputs surface in the UI.