DReichLab / DReichLab/AdmixTools
The results from F4-ratio and D-statistic are different
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Description
Dear @bumblenick
I have a few questions about the results from F4-ratio (qpF4ratio) and D-statistic (qpDstat). Can I detect introgression between two populations using F4-ratio on a genome-wide scale? I ran these two methods for a same dataset, as a result, the qpF4ratio detected EUR has about 1.1% introgression from IBEX1, but the qpDstat told me the IBEX1 share more derived allele with AFR. the topology among these five populations is following,
results from qpF4ratio version: 300
result: BEZ2 Outgroup EUR IBEX1 : BEZ2 Outgroup AFR IBEX1 0.988603 0.000951 1039.104
result: BEZ2 Outgroup AFR IBEX1 : BEZ2 Outgroup EUR IBEX1 1.011527 0.000973 1039.104
results from qpDstat version: 701
result: Outgroup IBEX1 EUR AFR 0.0045 0.001616 2.816 39371 39014 5123960
Can you help interpret this contradict results, many thanks!
Best Wishes
zhuqing
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Research direction
Start with the supplied topology and the qpF4ratio version 300 and qpDstat version 701 outputs. Compare the population ordering and the meaning of each statistic before assessing whether the results are actually contradictory. Done means providing a supported interpretation or identifying a reproducible defect.
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Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 15/100