Russki qpAdm result in admixtools2

[Russki]

The calculations are directly from SNPs, so the validity is incomparably higher than in Vahaduo.


target = c('russki')
left = c('Russia_Samara_EBA_Yamnaya', 'Italy_North_Villabruna_HG', 'Turkey_Barcin_LN.SG', 'Nganasan.HO')
right = c('Mbuti.DG', 'Ethiopia_4500BP', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG')
mypops = c('Mbuti.DG', 'Ethiopia_4500BP', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG', 'Russia_Samara_EBA_Yamnaya', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG', 'Turkey_Barcin_LN.SG', 'Nganasan.HO', 'russki')
results = qpadm(prefix, left, right, target, allsnps = TRUE)
results$weights
results$popdrop

Russki
53.9% Russia_Samara_EBA_Yamnaya
18.3% Italy_North_Villabruna_HG
23.1% Turkey_Barcin_LN.SG
4.69% Nganasan.HO

https://sun9-23.userapi.com/impg/BdQoN7PYDK-OZTU2tgj3rBPeUra4VVrrcgclnA/_1LSdlXMHXE.jpg?size=460x134&quality=95&sign=79e394a3c956a57170e197f636f6c673&type=album


I can demonstrate how other Europeans score in qpAdm (on a request).

If you want to have your own RAW data converted in a format readable for admixtools2, contact eupator (https://www.theapricity.com/forum/member.php?31189-eupator).

[rothaer]

Cool thing! Maybe you can make a brief guide for that tool.

- What program has to be used (downloaded)?
- Can it be run unter Windows or does it require Linux (or a Linuix Window like Ubuntu)?
- From where does one get the reference data?
- What is the data volume of a DNA kit for that usage?
- After I've made a WGS, is it possible to use more DNA data for both me and the references than what a common commercial DNA test yields (it's just abt. 0.02% of the entire genome)?

[Russki]

Cool thing! Maybe you can make a brief guide for that tool.

https://www.theapricity.com/forum/showthread.php?363817-admixtools2-TUTORIAL-for-WINDOWS

Skip the f2 commands.

my_f2_dir = "C:/Users/eupator/Downloads/eupator_qpAdm_files/my_f2_dir_eupator"
extract_f2(prefix, my_f2_dir, pops = mypops, overwrite = TRUE, maxmiss = 1)
f2_blocks = f2_from_precomp(my_f2_dir, pops = mypops, afprod = TRUE)


- What program has to be used (downloaded)?

RStudio.


- Can it be run unter Windows or does it require Linux (or a Linuix Window like Ubuntu)?

Can be run on Windows.


- From where does one get the reference data?

https://reichdata.hms.harvard.edu/pub/datasets/amh_repo/curated_releases/

[Token]

Looks neat, welcome to true genetic analysis. What is the chis-square and p-value of the model? They are the statistical tests that will show if your model is plausible or not.

Avoid including populations that are known to have experienced recent gene flow with one another since qpAdm assumes that there has been no gene flow between the left and right populations following the admixture event of interest. Czech_CordedWare and Armenia_LBA (both having undergone admixture with Yamnaya_Samara) shouldn't be in your pright list.