a new version of ADMIXTOOLS is out:
https://uqrmaie1.github.io/admixtools/index.html
it's faster and more user friendly.
has anybody tried it out yet?
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a new version of ADMIXTOOLS is out:
https://uqrmaie1.github.io/admixtools/index.html
it's faster and more user friendly.
has anybody tried it out yet?
https://i.imgur.com/bfvl1dE.png
I'm getting this error, i'm trying to figure out what's causing it.
this is when I filter out the missing SNPs (By default, extract_f2() will be very cautious and exclude all SNPs which are missing in any population):
https://i.imgur.com/ktVDjyS.png
populations used:
left
Russia_Sunghir6.SG
Greece_BA_Mycenaean
right
Russia_Afanasievo
Luxembourg_Loschbour
Russia_HG_Karelia
Anatolia_N
Poland_Globular_Amphora
Iran_GanjDareh_N
Kazakhstan_Eneolithic_Botai
Georgia_Kotias.SG
Morocco_Iberomaurusian
Nganasan
Papuan
Ami
ONG.SG
South_Africa_400BP.SG
Kenya_PastoralN
target
Serb
any recommendation is welcome.
I'm sure a certain Kurd will be active in this thread soon enough
Oh well. He will even destroy the font in this thread making it unreadably small :rolleyes:Quote:
Originally Posted by Dr_Maul
I don't really have a problem with Zoro unlike most people, however whatever he does to fuck up the thread font/size really gets the blood boiling...Quote:
Originally Posted by Leto
I saw it in Anthrogenica and I saved the link, but I don´t have used it already.Quote:
Originally Posted by vbnetkhio
according to this, Estonia BA passes as a Slavic proxy for Serbs (p-value 0.1) and the Hungarian Slavs don't (0.02 and 0.0006) :confused:
am I doing something wrong?
edit: I mixed up Estonia_IA and Estonia_BA. Estonia IA was Uralic admixed, Estonia BA was still purely Balto-Slavic, so it makes some sense after all.Code:pat wt dof chisq p f4rank Greece_BA_Mycenaean Estonia_BA.SG feasible best dofdiff chisqdiff p_nested
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <lgl> <lgl> <dbl> <dbl> <dbl>
1 00 0 15 20.6 1.50e- 1 1 0.480 0.520 TRUE NA NA NA NA
2 01 1 16 341. 7.57e-63 0 1 NA TRUE TRUE 0 36.2 0
3 10 1 16 305. 2.54e-55 0 NA 1 TRUE TRUE NA NA NA
pat wt dof chisq p f4rank Greece_BA_Mycenaean Hungary_AvarPeriod feasible best dofdiff chisqdiff p_nested
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <lgl> <lgl> <dbl> <dbl> <dbl>
1 00 0 15 27.5 2.52e- 2 1 0.255 0.745 TRUE NA NA NA NA
2 01 1 16 333. 3.24e-61 0 1 NA TRUE TRUE 0 292. 0
3 10 1 16 41.6 4.52e- 4 0 NA 1 TRUE TRUE NA NA NA
pat wt dof chisq p f4rank Russia_Sunghir6.SG Greece_BA_Mycenaean Hungary_Avar_daughter.or.mother.AV1 feasible best dofdiff chisqdiff p_nested
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <lgl> <lgl> <dbl> <dbl> <dbl>
1 000 0 14 15.5 3.43e- 1 2 0.670 0.347 -0.0176 FALSE NA NA NA NA
2 001 1 15 16.2 3.70e- 1 1 0.654 0.346 NA TRUE TRUE 0 -12.2 1
3 010 1 15 28.4 1.93e- 2 1 2.71 NA -1.71 FALSE TRUE 0 -10.7 1
4 100 1 15 39.1 6.19e- 4 1 NA 0.368 0.632 TRUE TRUE NA NA NA
5 011 2 16 50.0 2.29e- 5 0 1 NA NA TRUE NA NA NA NA
6 101 2 16 314. 3.55e-57 0 NA 1 NA TRUE NA NA NA NA
7 110 2 16 74.4 1.70e- 9 0 NA NA 1 TRUE NA NA NA NA
I think the outgroup set EurasianDNA used is good because they are high quality and have high SNP overlap with your test subjects plus they can differentiate streams of ancestry wellQuote:
Originally Posted by vbnetkhio
For Serbs you can start out with higher quality neolithic farmer samples + Iron gates Whg + relevant MLBA steppe + Iron age steppe/turkic
but is there anything obviously wrong with these outgroups? I used Afanasievo instead of Yamnaya because it's a larger and higher quality sample, and they seem to be of pure Yamnaya descent.Quote:
Originally Posted by Zoro
also Nganasan and Ami because admixture detects them as "pure" and important admixture sources, so they probably the purest descendants of some ancient populations we don't have samples of yet?
is it ok to do things like this?
Papuan, Nganassan, etc... are redundant since there will be no stream of ancestry from these pops to pleft.Quote:
Originally Posted by vbnetkhio
would Tianyuan and Devil's Cave samples be a better choice?Quote:
Originally Posted by Token
I'll check it out. I'm updating my operating system to a newer version it could take hours. This new version looks interesting.Quote:
Originally Posted by vbnetkhio
Is this different ? :
Full support for genotype data in PACKEDANCESTRYMAP/EIGENSTRAT format and PLINK format
So it will take just regular plink converted files now ? The documentation used to suck and especially for the Eigenstrat program or whatnot. That is where I got stuck If I remember correctly. I never got stuck with qpAdm I got stuck before that because the documentation sucked balls with converting files to Packagedancestrymap/Eigenstrat. However, if it just works with plink, at least with this new version, everything should be fine for me.
yep.Quote:
Originally Posted by JamesBond007
The opposite is true. In qpAdm you don’t want recent geneflow right to leftQuote:
Originally Posted by Token
We do actually have high quality WGS and diploid ancients. Yana ANS WGS and Kolyma-Mesol WGS and Devils-Gate-N Neo-Siberians such as Nganasan are descended from these. Ami have Devils-GateQuote:
Originally Posted by vbnetkhio
Anyways I would replace those ancient Africans with Mbuti because they have quality and SNP overlap issues
Also if you’re modelling Serbs with Neolithic and Chalcolithic keep your outgroups Neolithic and older
False. QpAdm assumes no streams from pleft into pright, so you choose 'deep' pops for pright to avoid violating this premise and not because you don't want recent geneflow from pright into pleft.Quote:
Originally Posted by Zoro
and how to intepret this?
the first 2 rows tell me that Estonia BA has WHG and EHG admixture, and the others just tell me that Estonia BA has steppe admixture.
how does this help me choose my outgroups?
- pop1 pop2 pop3 pop4 est se z p <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> 1 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Luxembourg_Loschbour 0.00514 0.000811 6.35 2.22e-10 2 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Russia_HG_Karelia 0.00316 0.000714 4.43 9.33e-6 3 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Anatolia_N -0.00744 0.000396 -18.8 1.63e-78 4 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Poland_Globular_Amphora -0.00546 0.000648 -8.43 3.60e-17 5 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Iran_GanjDareh_N -0.00437 0.000534 -8.17 3.08e-16 6 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Kazakhstan_Eneolithic_Botai 0.00196 0.000605 3.24 1.20e-3 7 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Georgia_Kotias.SG -0.00388 0.000768 -5.05 4.48e-7 8 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Morocco_Iberomaurusian -0.00490 0.000579 -8.47 2.41e-17 9 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Nganasan -0.00152 0.000456 -3.32 8.85e-4 10 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Papuan -0.00257 0.000545 -4.72 2.30e-6 11 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Ami -0.00195 0.000484 -4.03 5.64e-5 12 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo ONG.SG -0.00233 0.000579 -4.01 5.98e-5 13 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo South_Africa_400BP.SG -0.00319 0.000623 -5.12 2.99e-7 14 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Kenya_PastoralN -0.00571 0.000513 -11.1 8.98e-29 15 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Nepal_Samzdong_1500BP.SG -0.00204 0.000686 -2.97 2.99e-3 16 Greece_BA_Mycenaean Estonia_BA.SG Russia_Afanasievo Russia_OldBeringSea_Ekven -0.00108 0.000469 -2.30 2.15e-2
Are these potential sources of ancestry for pleft pops? If no, the you don't need them. If Sunghir shows some Siberian admixture (which can be tested with G25), then it might be a good idea to include Devils Gate.Quote:
Originally Posted by vbnetkhio
I’m out of here. You can thank and consult with ignoramus Token who has spent years doing qpAdm
Zoro is the typical case of a person who knows how to use qpAdm, but has no idea why he is using it that way.
well that's unfortunate, I wanted to hear both sides and try out both yours and his advice.Quote:
Originally Posted by Zoro
I plan to check later if any Siberian or Eastern Steppe samples fit into the model. But first i want to find the best sources for the Balto-Slavic and PaleoBalkan/Greco-Roman ancestry.Quote:
Originally Posted by Token
....
can you teach how to use it?Quote:
Originally Posted by vbnetkhio
first install rstudio:Quote:
Originally Posted by Kaazi
https://rstudio.com/products/rstudio/download/
then just follow these instructions:
https://uqrmaie1.github.io/admixtools/index.html
I got it working but it was a major pain in the ass like a death by a thousand paper cuts. Not using admixtools2 etc... per se but merging plink files and extracting them via Rstudio etc... I was hacking shell and perl scripts up all night etc.... jeez !
https://i.postimg.cc/fLvgnDBd/newplot.png
https://i.postimg.cc/65qbgsR7/newplot1.png
https://i.postimg.cc/SjbX6bbZ/weighted.png
Normal people can't do this shit you have to be either a geneticist or the tech geek eliteQuote:
Originally Posted by vbnetkhio
nice! are those reference populations from the Reich lab dataset? I can send you Danish, Irish, Welsh etc. if you are interestedQuote:
Originally Posted by JamesBond007
Yes, please, that would be great thanks ! Those reference populations are from a combination of HGDP and the 1,0000 genome project I merged them so it is likely they come from both projects but maybe most of them from one I'd have to double check if you want details.Quote:
Originally Posted by vbnetkhio
P.S. it is shame this thread is so dead but other stupid threads here are more popular ! :picard2:
this dataset has Welsh samples:Quote:
Originally Posted by JamesBond007
https://evolbio.ut.ee/Ongaro_2019/
German:
https://evolbio.ut.ee/turkic/
Swedish:
https://evolbio.ut.ee/khazar/
i'll send you the rest later
Ok, thanks a lot man. :thumb001:Quote:
Originally Posted by vbnetkhio
I want to know if playing in qpadm only with modern samples is "valid" methodology. Outside TA all people discussing qpadm use only ancient samples.
But honestly I am much more interested in modern admixtures.
it 's validQuote:
Originally Posted by Lucas
here on page 91 onwards they start modelling with moderns:
https://www.ncbi.nlm.nih.gov/pmc/art...Supplement.pdf
they also use moderns as outgroups:
Quote:
From Imperial period onward
To further increase the power to find best fit models for samples in Imperial era and later in qpAdm
analysis, we defined an additional “right” (outgroup) population set consisting of 18 diverse modern
populations (MOD18) (with the sample size indicated by the number in the parentheses):
Ami (10), Basque (29), BedouinB (19), Biaka (20), Bougainville (2), Chukchi (20), Eskimo_Naukan (12),
Han (43), Iranian (38), Ju-hoan_North (5), Karitiana (12), Mbuti (10), Papuan (14), Russian (22),
Sardinian (27), She (10), Ulchi (25), Yoruba (30).
As for earlier time periods, we performed qpAdm admixture modeling for Italian individuals sampled in
Imperial era and later in a stepwise fashion. Having observed the high inter-individual ancestry diversity
in Iron Age and after, we did not test one-way models, as a positive result (p>0.05) would only indicate
that the average ancestries of the sampled individuals from the two populations happened to be similar.
Instead, we tested two-way models for individual in each time period, proposing the two sources to be
preceding Italian samples in last period and another ancient population (Iron Age onward) or a modern
population. We considered a model to be acceptable if it has p>0.05 with both ANC17 and MOD18 as the
right set, and reported the results under MOD18, unless otherwise noted.
It is a matter of statistics I'd venture to guess maybe some statistical methods are valid or 'more valid' than others when dealing with modern populations. It is really a math issue here not the tool itself IMHO but I'm not a mathematician.Quote:
Originally Posted by Lucas
Ok I’ll give a 2nd chance but any wise guy comments from him or anyone else who thinks they know better and I’m out for good.Quote:
Originally Posted by vbnetkhio
YesQuote:
Originally Posted by Lucas
QpAdm is a powerful tool in modelling present-day pops as admixtures of other present-day pops except perhaps in situations of continuous geneflow over an extended period of timeQuote:
Originally Posted by JamesBond007
Nothing more than a reflection of the type of audience here. Looks like just a handful of people interested in more serious analysis, or are able to understand serious analysis in the first placeQuote:
Originally Posted by JamesBond007