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Pull request overview
This PR adds ADMIXTURE-based workflows for All of Us (AoU) ancestry analysis and local ancestry reference testing. These workflows complement existing Rye-based estimation by providing an alternative approach that addresses population overestimation biases observed in the Rye method.
Changes:
- Added
run_admixture.wdlworkflow for unsupervised ancestry clustering using ADMIXTURE software - Added
convert_vcf_to_plink_bed.wdlworkflow to convert VCF files to PLINK binary format - Added comprehensive README documentation explaining the three admixture workflows and their trade-offs
- Updated
.dockstore.ymlto register the new workflows
Reviewed changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| all_of_us/admixture/run_admixture.wdl | Implements ADMIXTURE workflow with parameterized K value and CPU/memory settings |
| all_of_us/admixture/run_admixture.changelog.md | Documents version history for run_admixture workflow |
| all_of_us/admixture/convert_vcf_to_plink_bed.wdl | Implements VCF to PLINK conversion using PLINK software |
| all_of_us/admixture/convert_vcf_to_plink_bed.changelog.md | Documents version history for convert_vcf_to_plink_bed workflow |
| all_of_us/admixture/README.md | Provides comprehensive documentation of all three admixture workflows |
| .dockstore.yml | Registers the two new workflows in Dockstore |
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Remember to squash merge! |
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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jessicaway
approved these changes
Jan 29, 2026
jessicaway
reviewed
Jan 29, 2026
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| # CMRG Variant Calling Workflows (WDL) |
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Should "challenging medically relevant genes (CMRG)" be in here at least once
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yes, yes it should. Thank you!
rsc3
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Addig admixture workflows used for both AoU admixture analyses and local ancestry initial reference testing