qpAdm thread

[vbnetkhio]

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?

[vbnetkhio]

I'm getting this error, i'm trying to figure out what's causing it.

[vbnetkhio]

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):

[vbnetkhio]

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.

[Dr_Maul]

I'm sure a certain Kurd will be active in this thread soon enough

[Leto]

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

[Dr_Maul]

Oh well. He will even destroy the font in this thread making it unreadably small

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...

[gixajo]

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?

I saw it in Anthrogenica and I saved the link, but I don´t have used it already.

[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)
am I doing something wrong?

  pat      wt   dof chisq        p f4rank Greece_BA_Mycenaean Estonia_BA.SG feasible best  dofdiff chisqdiff p_nested
                                                    
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
                                                         
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
                                                                                        
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

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.

[Zoro]

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 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 well

For Serbs you can start out with higher quality neolithic farmer samples + Iron gates Whg + relevant MLBA steppe + Iron age steppe/turkic