Skip to content

Miner

Miner is the clinical genomics service for managing orders, subjects, samples, and variant interpretation.

Features

  • Subject Management: Create and track patients with clinical metadata
  • Sample Management: Create samples linked to subjects with specimen details
  • Order Management: Create and track clinical orders with samples
  • Sampleinfo Generation: Generate pipeline-ready JSON from subject + sample metadata
  • Samplesheet Generation: Generate nf-core compatible CSV from order samples
  • Variant Browser: Browse and filter variants from VCF files with tier-based views
  • Variant Interpretation: Detailed variant pages with clinical evidence and classifications
  • Manual Classification: Expert review and manual AMP/ASCO/CAP tier assignment

CLI Access

All miner entities can be managed via the iflow CLI:

iflow subjects create -n "Patient Smith" -P sex=female -P first_name=Jane
iflow samples create --subject-id SUBJ_ID -n "NA12878" -P sample_type=germline
iflow orders create -n "Case 001" --priority urgent
iflow orders add-sample ORDER_ID SAMPLE_ID
iflow samples sampleinfo SAMPLE_ID
iflow orders samplesheet ORDER_ID

See the CLI guides: Subjects | Samples | Orders

API Access

REST API at https://miner.flow.labpgx.com/api/v1/:

Endpoint Description
/subjects Subject CRUD
/samples Sample CRUD
/samples/{id}/sampleinfo Pipeline-ready JSON
/orders Order CRUD
/orders/{id}/samplesheet nf-core samplesheet CSV

See API Reference for full endpoint documentation.

Documentation