DReichLab / DReichLab/AdmixTools
qpDstats produced strange results for some combination of species
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Description
Hi,
I am using qpdstats in admixtools to detect introgression among species.
I used convertVCFtoEigenstrat.sh script to convert vcf file to eigenstrat file format, and assigned each individual to a population. When I perform the qpDstats, it seems some analyses runs fine, but others just show 0, and the ones run fine were all significant, could anybody tell what's the problem?
Here is part of my result:
W | X | Y | Z | D | stderr | Zscore | BABA | ABBA | nsnps
| 1 | Med | CN | AU | EU | 0 | 1 | 0 | 0 | 0 | 0 |
|---|---|---|---|---|---|---|---|---|---|---|
| 2 | Med | CN | AU | Usland | 0 | 1 | 0 | 0 | 0 | 0 |
| 3 | Med | CN | AU | Usnat | 0 | 1 | 0 | 0 | 0 | 0 |
| 4 | Med | CN | AU | OG | 0 | 1 | 0 | 0 | 0 | 0 |
| 5 | Med | CN | EU | AU | 0 | 1 | 0 | 0 | 0 | 0 |
| 6 | Med | CN | EU | Usland | 0 | 1 | 0 | 0 | 0 | 0 |
| 7 | Med | CN | EU | Usnat | 0 | 1 | 0 | 0 | 0 | 0 |
| 8 | Med | CN | EU | OG | 0 | 1 | 0 | 0 | 0 | 0 |
| 9 | Med | CN | Usland | AU | 0 | 1 | 0 | 0 | 0 | 0 |
| 10 | Med | CN | Usland | EU | 0 | 1 | 0 | 0 | 0 | 0 |
| 37 | Med | AU | OG | CN | 0 | 1 | 0 | 0 | 0 | 0 |
| 38 | Med | AU | OG | EU | 0 | 1 | 0 | 0 | 0 | 0 |
| 39 | Med | AU | OG | Usland | 0 | 1 | 0 | 0 | 0 | 0 |
| 40 | Med | AU | OG | Usnat | 0 | 1 | 0 | 0 | 0 | 0 |
| 41 | Med | EU | CN | AU | 0 | 1 | 0 | 0 | 0 | 0 |
| 42 | Med | EU | CN | Usland | -0,3349 | 0,035253 | -9,5 | 2485 | 4986 | 214014 |
Thanks,
Cui
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Research direction
Start by reviewing the qpDstats invocation and the population assignments produced while using convertVCFtoEigenstrat.sh. Compare the analyses with zero counts against the significant result, including the Eigenstrat inputs and reported nsnps values. Done means identifying the cause of the inconsistent output and confirming the correction with the affected species combinations.
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Assessment
- Tech stack
- c, shell
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100