Initial release: rarelens platform skeleton (AGPL-3.0)

End-to-end variant interpretation platform for rare genetic disease research:
SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline,
LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure.
Public test data only; no clinical claims.

data/README.md

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+# Test data
+
+No patient data. Use public sources only:
+
+- ClinVar VCF (GRCh38): https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/
+- gnomAD exomes subset for allele frequencies
+- A small HG002 (GIAB) chr22 slice for a realistic germline sample
+
+```bash
+# Example: 2,000 ClinVar variants on chr22 as a smoke-test VCF
+wget -O clinvar.vcf.gz https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
+tabix -p vcf clinvar.vcf.gz
+bcftools view -r 22 clinvar.vcf.gz | bcftools view -H | head -2000 > body.vcf
+(bcftools view -h clinvar.vcf.gz; cat body.vcf) | bgzip > example.vcf.gz
+tabix -p vcf example.vcf.gz
+```