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