DReichLab / DReichLab/AdmixTools
Extension of model-based clustering methods
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- Dominant language
- C
- Stars
- 235
- Forks
- 76
- PR merge metrics
- No merged PRs in 30d
Description
@bumblenick
accounting for differential drift between populations.
Currently available programs such as ADMIXTURE and STRUCTURE are sensitive to differential drift so I wonder if perhaps something using formal statistics like QpAdm(or perhaps that new method) but at the same being able to create genetic clusters like ADMIXTURE is possible. Or something being able to test genetic drift on separate model-based genetic components detected in a given sample, not the whole genome like current programs are doing. I think that would be particularly useful for Paleolithic specimens who according to ADMIXTURE were extremely "mixed". Is that because they weren't fully genetically differentiated yet? Which may complicate correctly detecting their relation to even Mesolithic samples such as WHGs let alone younger populations.
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Research direction
The issue names no files, tests, or entry points. First review the existing AdmixTools methods and compare the requested behavior with ADMIXTURE, STRUCTURE, and qpAdm. Done would require a defined method that accounts for differential drift while producing model-based genetic clusters, with results tested on relevant Paleolithic and later populations.
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Assessment
- Tech stack
- c
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100