glebis Genome Import
Import raw genome data from any supported DTC provider or VCF file.
Vault Configuration
- Config:
$GENOME_VAULT_ROOTor config/default.yaml - Database:
data/genome.db - Raw data:
data/raw/(user places their file here) - Provider detection:
config/provider_formats.yaml
Sub-Workflows
A: Raw Import (default)
- Auto-detect provider: Run
python3 scripts/genome_init.py --detect-only <file> - Confirm with user: Show detected provider, assembly, confidence
- Import: Run
python3 scripts/genome_init.py <file> --profile <name> - Show QC report: total SNPs, filtered, chromosome distribution
- Suggest next steps: onboarding or imputation
B: Imputation Preparation
Triggered by: "prepare for imputation", "I want to impute"
- Export VCF: Generate imputation-ready VCF from SQLite
python3 scripts/prepare_for_imputation.py - REF/ALT normalization (requires bcftools):
bcftools norm --check-ref ws --fasta-ref hg19.fa output.vcf -o normalized.vcf - Pre-upload checklist:
- VCF generated and validated
- REF/ALT normalized against reference genome
- Chromosome naming correct for target server
- File compressed with bgzip (optional)
- Server guidance: Show comparison table (Michigan vs TOPMed vs Sanger)
- Known gotchas:
- Michigan requires >= 20 samples (duplicate sample column as workaround)
- HRC r1.1 for EUR, TOPMed r3 for diverse ancestry
- Processing: 2-12 hours
- Results encrypted, deleted after 7 days
C: Post-Imputation Import
Triggered by: "import imputed data", user provides VCF files
- Locate imputed VCFs: Check
data/output/imputed/or ask user - Import: Run
python3 scripts/genome_init.py <vcf> --min-r2 0.3 - Quality report: Show r² distribution (high/good/moderate/low)
- Suggest: Re-run PRS, check gap coverage, update gene notes
D: Troubleshooting
Common issues and fixes:
- Allele switches: Run
bcftools norm --check-ref wsbefore upload - Chromosome naming: UCSC uses
chr1, HRC expects bare1 - 20-sample minimum: Duplicate sample column 20x in VCF header
- Low overlap: Check assembly match (GRCh37 vs GRCh38)
Supported Providers
| Provider | Format | Assembly | Detection |
|---|---|---|---|
| 23andMe v4/v5 | TSV (4 cols) | GRCh37 | "23andMe" in comments |
| AncestryDNA | TSV (5 cols) | GRCh37 | allele1/allele2 columns |
| MyHeritage | CSV (4 cols) | GRCh37 | "RSID,CHROMOSOME,POSITION,RESULT" |
| Nebula | VCF | from header | "source=Nebula" |
| Generic VCF | VCF | from header | "##fileformat=VCF" |
Output
- Populated SQLite database with profile and import tracking
- QC report (console + optional markdown)
- Next step recommendations