https://github.com/lieberinstitute/nda-dbgap
establishing NDA and dbGaP data submission protocols
https://github.com/lieberinstitute/nda-dbgap
Last synced: 10 days ago
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establishing NDA and dbGaP data submission protocols
- Host: GitHub
- URL: https://github.com/lieberinstitute/nda-dbgap
- Owner: LieberInstitute
- Created: 2026-07-01T18:01:22.000Z (24 days ago)
- Default Branch: devel
- Last Pushed: 2026-07-06T00:43:56.000Z (19 days ago)
- Last Synced: 2026-07-12T04:41:51.646Z (13 days ago)
- Language: Python
- Size: 590 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Agents: AGENTS.md
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README
# NDA and dbGaP data submission SOP
This repository documents and develops a reproducible workflow for preparing LIBD controlled-access data submissions to the NIMH Data Archive (NDA), with dbGaP registration/linkage tracked where required for human genomic data.
The first worked example is SNP-array genotype data preparation for the union of:
- SCZ-PNN donors represented by NDA Study `3054`
- MBv donors represented by Ryan's `119`-row MBv donor/sample list
- overlapping donors/controls deduplicated before packaging
## Current goal
Prepare, validate, and submit a genotype data package to NDA collection `C5229`, while documenting the process well enough to become a reusable SOP.
Parallel discovery work:
- understand Ryan Miller's existing NDA data packaging work for collection `C5229`
- inspect whether MBv Visium prep exists on JHPCE for experiment `2863`
- prepare genotype inputs on `srv16` from the documented genotype locations
- determine how the NDA genotype submission should link to NDA Studies, Experiments, Submissions, and the dbGaP record
## Documentation map
- `docs/NDA-collection-info.md` - current interpretation of collection `C5229`, including Studies, Experiments, Submissions, counts, and open mapping questions.
- `docs/workstreams.md` - live tracker for active workstreams, blockers, evidence, and next actions.
- `docs/sop-nda-genotype-submission.md` - discovery-stage SOP for NDA genotype package preparation, validation, and submission.
- `docs/sop-nda-genotype-data-package.md` - neutral command-level guide for preparing an NDA genotype package from VCF inputs and donor/GUID metadata.
- `docs/handoffs/jhpce-srv16-nda-genotype-handoff.md` - handoff for JHPCE Ryan/MBv package discovery and srv16 genotype package preparation.
## Controlled data rules
Do not commit controlled donor-level or genotype data.
Do not commit:
- donor rows
- BrNum row lists, unless explicitly approved
- GUID or pseudo-GUID crosswalks
- NDA downloads
- genotype files
- local validation outputs containing donor identifiers
- archive files or package payloads
Safe to commit:
- SOP documentation
- aggregate counts
- non-sensitive command patterns
- high-level path references needed for reproducibility
- notes that explicitly avoid donor rows and GUID mappings
BrNums may be used in local work or chat when needed.
Generated local working directories for controlled files should stay untracked.