Open-data manifest
15 sources · D01–D15
Mac Studio · local-mac profile · /Volumes/CGT_POC
total sources
15
scripted
10
manual
4
api
1
Priority A1
6 sources
D011000 Genomes 30x (NYGC)
okPopulation-scale WGS reference, including SEA samples
https://www.internationalgenome.org/data-portal/data-collection/30x-grch38local path/Volumes/CGT_POC/raw/D01_1KG_30x/
raw files*.cram · *.crai · per-sample sequencing
derivedphased BCF · ancestry PCs
licenseOpen · IGSR data sharing policy
scriptedsha256 ✓
Pull only SAS + EAS first to fit local disk; 700 GB
status checked 2026-07-06view details
D021KGP sample metadata
okPopulation labels, sex, relatedness for ancestry partitioning
https://www.internationalgenome.org/data-portal/samplelocal path/Volumes/CGT_POC/raw/D02_1KG_meta/
raw filesigsr_samples.tsv
derivedpop_labels.parquet
licenseOpen
scriptedsha256 ✓
Pin SHA-256; metadata changes occasionally
status checked 2026-07-06view details
D03gnomAD v4.1
okPopulation allele frequencies; rare-variant filter
https://gnomad.broadinstitute.org/downloadslocal path/Volumes/CGT_POC/raw/D03_gnomAD_v4.1/
raw filesgnomad.exomes.v4.1.sites.*.vcf.bgz
derivedaf_lookup.parquet
licenseOpen (CC0)
scriptedsha256 ✓
Chunk by chromosome; 1.4 TB full release
status checked 2026-07-06view details
D04ClinVar
okClinical interpretation of variants in HBB, BCL11A, HBS1L-MYB
https://www.ncbi.nlm.nih.gov/clinvar/local path/Volumes/CGT_POC/raw/D04_ClinVar/
raw filesclinvar.vcf.gz · variant_summary.txt.gz
derivedclinvar_hbb.parquet
licensePublic domain
scriptedsha256 ✓
Monthly refresh; lock release date in manifest
status checked 2026-07-06view details
D05HbVar
manual pendingCurated hemoglobin variant catalog (β/α/HbE)
https://globin.bx.psu.edu/hbvar/local path/Volumes/CGT_POC/raw/D05_HbVar/
raw fileshbvar_export.tsv (manual)
derivedhbvar_curated.parquet
licenseAcademic use · cite Hardison 2002
manualsha256 …
Set calendar reminder; no API. Track export date.
status checked 2026-07-06view details
D06IthaGenes
manual pendingThalassemia-specific variant + phenotype database
https://www.ithanet.eu/db/ithageneslocal path/Volumes/CGT_POC/raw/D06_IthaGenes/
raw filesithagenes_export.csv (manual)
derivedithagenes_curated.parquet
licenseAcademic use · cite Kountouris 2014
manualsha256 …
Email custodian if export is gated; SEA subset preferred
status checked 2026-07-06view details
Priority A2
5 sources
D07GWAS Catalog
okTrait-associated variants (HbF, transfusion response)
https://www.ebi.ac.uk/gwas/local path/Volumes/CGT_POC/raw/D07_GWAS_Catalog/
raw filesgwas-catalog-associations_ontology-annotated.tsv
derivedgwas_hbf_filtered.parquet
licenseOpen · EBI terms
scriptedsha256 ✓
Filter EFO_0004541 (HbF level) before merge
status checked 2026-07-06view details
D08PGS Catalog
okPolygenic score weights for transferability checks (G02)
https://www.pgscatalog.org/local path/Volumes/CGT_POC/raw/D08_PGS_Catalog/
raw filesPGS*.txt.gz scoring files
derivedprs_weights.parquet
licenseOpen · per-score citation required
scriptedsha256 ✓
Pin score IDs in config/scores.yaml
status checked 2026-07-06view details
D09Ensembl VEP cache
okVariant annotation (consequence, gene, regulatory)
https://www.ensembl.org/info/docs/tools/vep/local path/Volumes/CGT_POC/raw/D09_VEP_cache/
raw fileshomo_sapiens_vep_112_GRCh38.tar.gz
derivedannotated.vcf.gz
licenseApache 2.0
scriptedsha256 ✓
Cache 25 GB; pin VEP release 112
status checked 2026-07-06view details
D10AFND (Allele Frequency Net Database)
manual pendingHLA + KIR allele frequencies for Thai/SEA populations
http://www.allelefrequencies.net/local path/Volumes/CGT_POC/raw/D10_AFND/
raw filesafnd_thai_hla.tsv (manual)
derivedhla_af_thai.parquet
licenseAcademic use · cite Gonzalez-Galarza 2020
manualsha256 …
No bulk download; one population at a time
status checked 2026-07-06view details
D11PharmCAT
okPharmacogenomic call layer (GSTA1, CYP, etc.) — informational only (G08)
https://pharmcat.clinpgx.org/local path/Volumes/CGT_POC/raw/D11_PharmCAT/
raw filespharmcat-3.2.0-all.jar + reference data
derivedpgx_calls.json
licenseMPL 2.0
scriptedsha256 ✓
Moved to pharmcat.clinpgx.org; jar asset is now versioned (v3.2.0). No dosing surfaced; calls only (G08)
status checked 2026-07-06view details
Priority Reference
3 sources
D12CHMMOTv1 (chromatin annotations)
okRegulatory context for BCL11A enhancer + HBB locus
https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.htmllocal path/Volumes/CGT_POC/raw/D12_CHMMOTv1/
raw filesE*_18_CALLS_segments.bed.gz
derivedreg_context.parquet
licenseRoadmap Epigenomics terms
scriptedsha256 ✓
Erythroid + CD34 tracks only; ignore brain tissues
status checked 2026-07-06view details
D13β-thal platelet WGS (Tang 2024)
verifyTranscriptomic context; megakaryocyte/erythroid axis
https://www.ebi.ac.uk/ena/browser/view/PRJEB12345local path/Volumes/CGT_POC/raw/D13_platelet_WGS/
raw files*.fastq.gz · per-sample
derivedplatelet_expression.parquet
licenseOpen · ENA accession terms
scriptedsha256 …
PLACEHOLDER: accession PRJEB12345 resolves to an unrelated Aeromonas study, not the cited Tang 2024 dataset. Replace with the real accession before use. Transcriptomic component is v1.1+ contingent (not in the locked ensemble).
status checked 2026-07-06view details
D14Nuinoon 2010 Thai cohort
manual pendingHistorical Thai β-thal GWAS summary (legacy comparator)
https://doi.org/10.1007/s00439-009-0770-2local path/Volumes/CGT_POC/raw/D14_Nuinoon2010/
raw filessupplementary tables (PDF/XLSX)
derivednuinoon_legacy.parquet
licensePublisher terms · cite Nuinoon 2010
manualsha256 …
DOI resolves to Springer; supplement is a manual publisher download. Cross-reference vs gnomAD AFs
status checked 2026-07-06view details
Priority Optional
1 source
D15LDlink
okInteractive LD lookups for tag SNP selection
https://ldlink.nih.gov/local path/Volumes/CGT_POC/cache/D15_LDlink/
raw filesAPI JSON responses
derivedld_lookup.parquet
licenseOpen · token required
api
Rate-limited; cache responses keyed on rsID pair
status checked 2026-07-06view details
Source: Mac Studio Working Sheet v2.0 · Data_Manifest tab · 28 May 2026