This bad news Nebula genomics its will closed in 4 February 2025
if you take test in Nebula genomics  , don't forget to download all information BAM and Fastq
https://www.reddit.com/r/Nebulagenomics/...ry_4_2025/

I just came to a very unexpected discovery:
For the hg CT: this is a very short "trunk" segment with just 5 or 6 snips.
It is the transition from CDE haplogroups to the next F.

hg37 positions: (Build 37 #)

Y:7921525
Y:15961200 (not listed in ISSOG CT )
Y:16262390
Y:18607673
Y:22850240

The unexpected discovery is , these snips are also presented in an earlier individual from Haplogroup B4.

The individual is:
10 GS000001807-ASM Hadza5 Hadza B4

That means we should talk not about CT, but an earlier group B4-T from which we have the next CDE  / CT / F .

Is anyone able to validate on this ?

r/23andMe- Latinos in the US Admixture Genetic Study (archive)

Quote:This study includes thousands of participants and admixture results broken down by different countries of origin. Link to full publication: https://www.sciencedirect.com/science/ar...7724001167

Quote:Study participant stats… Some were born in the US, most were not.

Quote:Advancements in genetic research by the Hispanic Community Health Study/Study of Latinos: A 10-year retrospective review
https://doi.org/10.1016/j.xhgg.2024.100376

The Hispanic Community Health Study/Study of Latinos (HCHS/SOL) is a multicenter, longitudinal cohort study designed to evaluate environmental, lifestyle, and genetic risk factors as they relate to cardiometabolic and other chronic diseases among Hispanic/Latino populations in the United States. Since the study’s inception in 2008, as a result of the study’s robust genetic measures, HCHS/SOL has facilitated major contributions to the field of genetic research. This 10-year retrospective review highlights the major findings for genotype-phenotype relationships and advancements in statistical methods owing to the HCHS/SOL. Furthermore, we discuss the ethical and societal challenges of genetic research, especially among Hispanic/Latino adults in the United States. Continued genetic research, ancillary study expansion, and consortia collaboration through HCHS/SOL will further drive knowledge and advancements in human genetics research.

I would like to share with you some data that I was able to convert from the raw data. 
 From the already published data,  I converted the data for 2 Neanderthals and created 2 plink files that you can test further for other analysys. 

The main goal for me was to convert such raw data into plink compatible data / v. 1240k /, but also to annotate  called vcf files  into other available datasets. ( like the dataset published by Karmin ).
As a result of such processing I was able to create plink files for 2 Neanderthals with medium to high coverage with   more than 50% which can be used for other tests like PCA and qpadm.

Also my goal was to generate the data for Y-chromosome and to replicate the results from the original publications.
Here is the raw data:
 
Chagyrskaya02
https://www.ebi.ac.uk/ena/browser/view/S...show=reads
from:
https://www.nature.com/articles/s41586-022-05283-y#Tab1

 Mezmaiskaya2
https://www.nature.com/articles/s41586-0...3-y#MOESM1
https://www.ebi.ac.uk/ena/browser/view/PRJEB55327


I was able to obtain better data for  Mezmaiskaya2, however for  Chagyrskaya02 the Y-CHR data is much better.  More details how this data was processed you should check with the original publication.
I used usegalaxy to convert the raw data into bcf and then   plink  into /bed, bim, fam / format.


Here is the link to share the converted data:

https://ufile.io/3u28nlzm
This data should be valid to create G25 .
I will provide additional details .

what method is used to scale coordinates, I'm trying to scale raw coordinates but it's not scaling correctly

Hello, in this thread I want to discuss the Ancient North African (ANA) and Basal Eurasian (BE) lienages, their phylogenetic position, and their legacy on modern populations.

Basically, African and Eurasian phylogeny (geneflow excluded; just primary ancestry):
   

E.g. the first deep divergences gave rise to SAHG (South African hunter-gatherers), CAHG (Central African hunter-gatherers), WAHG (West African hunter-gatherers; + some archaic ghost), and the ancestor of Ancient East Africans/Trans-Sahelians and the PreOoA group.

Trans-Sahelians than diverged into the group which would later became ancestral to Nilo-Saharan speakers, and a group representing the main ancestry of later "Neo West Africans".

Similarly, the PreOoA group diverged into the OoA exit group and a group broadly ancestral to the Mota HG (+something deep/SAHG-like) and modern Omotic-speakers, as well as Ancient North Africans (ANA). ANA may have absorbed small amounts of deep ghost ancestry (North African_MSA or early Aterian). Later constituting the main ancestry for Iberomaurusians and similar populations. The Mota/ANA ancestral clade (dubbed Northeast African HG) would be the main source for the initial spread of haplogroup E and likely D0, while C, D1 and F were spread by the OoA exit group.

ANA geneflow into the Trans-Sahelian group ancestral to Neo West Africans (e.g. its western branch), introduced haplogroup E (E1b1a clade). Later on, this Neo West African group absorbed the local West African hunter-gatherers (WAHG) resulting in the formation of modern West Africans (e.g. Niger Congo speakers such as Yoruba). E1b1a underwent a founder effect, becoming dominant, while A3, B were reduced to lower frequency.

Regarding the OoA group, after the OoA exit, Basal Eurasians (BE) diverged from the main group, becoming isolated on the Arab peninsula, especially the still unsunken Persian Gulf region, and did not receive archaic admixture. Basal Eurasian ancestry formed the main ancestry for Upper Paleolithic Iran and still made up roughly 50% for Iran_HG and Iran_N like groups (48-62%).
   

E.g.:
   

The model:
   

-> As explained above, Ancient North African (ANA), and the main source for Mota_HG, represents a lineage which forms a sister clade to Eurasians/OoA to the exclusion of other African lineages, but which stayed in Africa, not having underwent the OoA drift. – Appearently, Mota_HG has also deep SAHG-like admixture (~29%) absent from the ANA source of Iberomaurusians, although there may be some small MSA input.

ANA-like ancestry and its dispersal correlate with the initial spread of haplogroup E (and likely D0). Evident for Mota, modern Omotic-speakers, Iberomaurusians, Natufians, and Afroasiatic-speaking groups in general. – The presence of subclade E1b1a among modern West Africans seems to correlate with an admixture and founder effect, especially when looking into the presence of other clades e.g. A3 or B and their dominace among Nilo-Saharan speakers (e.g. Gumuz or Nuer etc.).

This fits with previous Maximum likelyhood trees and other models:
   
   

Summary

Ancient North Africans "ANA" (and the main ancestry of Mota_HG) represents a sister lineage of the OoA group (Eurasians) which did not participate in the OoA exit, but stayed in Northeast Africa. This lineage correlates with the initial spread of haplogroup E and D0.

Basal Eurasians diverged from other Common or Crown Eurasians after the OoA exist and became isolated in the Gulf region. This also fits with the high Basal ancestry of Iran_N/HGs. Appearently, the deep ancestry among Iran_N and Natufians is distinct. Basal Eurasian ancestry may correlate with the initial spread of haplogroup G and H (?).

Quote:-23andMe has been exploring a possible sale of its telehealth business, Business Insider has learned.
-The struggling health company bought the virtual-care startup Lemonaid in 2021 for $400 million.
-23andMe's stock plummeted after a 2023 data breach exposed millions of customer accounts.

I have a Linux Ubuntu Virtual Machine, I use it for running Admixture etc. Last time I used it everything was okay but now there are errors:







Does anyone know what might be wrong and how to fix it?

https://www.exploreyourdna.com/calculato...cinski.htm

This calculator has been out for a while now but I think it’s one of the better ones for the many references it has. Sometimes I like adding and removing populations to see different ways of how calculators view my ancestry.


I’m an old stock American of English, Scottish (Ulster-Scots) and older French Huguenot ancestry. When modeling myself with this calculator I have a heavy draw toward Caledonian Scotland:

Target: Garimund_scaled
Distance: 1.4490% / 0.01448985
40.2 Europe_Northwest:Caledonian_Scotland
33.0 Europe_Southwest:Celtiberians
18.8 Europe_Northwest:North_Germanic
4.8 Europe_Southwest:Cantabri_Confederacy
1.6 Caucasus_Colchis_Kingdom
0.8 Africa_Cushitic_Peoples
0.4 Africa(South)_Khoisan_Peoples
0.4 Africa_Garamantians

Caledonians always carry some weight in calculators for me so I wanted to see myself without them:

Target: Garimund_scaled
Distance: 1.5741% / 0.01574114
35.6 Europe_Southwest:Celtiberians
30.8 Europe_Northwest:North_Germanic
25.0 Europe_Northwest:Brittonic_EnglandN
5.4 Europe_Southwest:Cantabri_Confederacy
1.8 Caucasus_Colchis_Kingdom
1.0 Africa_Cushitic_Peoples
0.4 Africa(South)_Khoisan_Peoples

With such a large regional sample base to pick from, I think it’s pretty cool seeing how this wants to view my ancestry as either Caledonian>North Germanic OR Brittonic Northern England & North Germanic. Having a good bit of Ulster Scots ancestry, which basically has Pictish/Gaelic, Cumbric, Northumbrian and Danelaw elements, I think this is pretty cool to see. 

https://www.nature.com/articles/s41586-024-08409-6?