kemal
5463f489a3
ci / api (push) Failing after 10s
ci / terraform (push) Failing after 11s
ci / web (push) Failing after 35s
ci / pipeline (push) Failing after 2m29s
ci / images (api) (push) Skipped
ci / images (ml) (push) Skipped
ci / images (pipeline) (push) Skipped
ci / images (web) (push) Skipped
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.
619 B
619 B
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
# 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