Allentoft Population Genomics of Late Stone Age West Eurasia

[ChrisR]

Published: 10 January 2024
Population genomics of post-glacial western Eurasia
... we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. ...
https://doi.org/10.1038/s41586-023-06865-0

Sorry if obvious to others, but is all raw data (except the 100 Danish genomes?) already public since months including in Eurogenes G25 values or has some still to be published (now with the official article)?

[Anglesqueville]

Published: 10 January 2024
Population genomics of post-glacial western Eurasia
... we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. ...
https://doi.org/10.1038/s41586-023-06865-0

Sorry if obvious to others, but is all raw data (except the 100 Danish genomes?) already public since months including in Eurogenes G25 values or has some still to be published (now with the official article)?

https://erda.ku.dk/archives/917f1ac64148...chive.html

That's it for the data (imputed and non-imputed), one file (.vcf) per chromosome. I seem to remember that the variants are not encoded with their rsid, and that I had to redo the coding of the names. In addition, you must also enter the names of populations. I haven't checked, but I believe that everyone in the study is there (except perhaps a handful who had too low coverage). If necessary I can provide an eigenstrat file reduced to 1240K with the usual codings. For G25 I don't know.

[ChrisR]

For G25 I don't know.

I checked some of the used IDs like NEO828, NEO143, NEO816, NEO806 in the latest Global25_PCA_scaled.txt and could not find them. Unclear to me if Davidski can or do not want to use the provided data format or if some other type of data might get available (to him).
Beside the terminal Y-Haplogroups I'm mostly interested in G25 values (or K13 etc.) to include in my low level comparisons.

[teepean]

For G25 I don't know.

I checked some of the used IDs like NEO828, NEO143, NEO816, NEO806 in the latest Global25_PCA_scaled.txt and could not find them. Unclear to me if Davidski can or do not want to use the provided data format or if some other type of data might get available (to him).
Beside the terminal Y-Haplogroups I'm mostly interested in G25 values (or K13 etc.) to include in my low level comparisons.

The samples might have had low coverage.

[teepean]

Published: 10 January 2024
Population genomics of post-glacial western Eurasia
... we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. ...
https://doi.org/10.1038/s41586-023-06865-0

Sorry if obvious to others, but is all raw data (except the 100 Danish genomes?) already public since months including in Eurogenes G25 values or has some still to be published (now with the official article)?

https://erda.ku.dk/archives/917f1ac64148...chive.html

If necessary I can provide an eigenstrat file reduced to 1240K with the usual codings. For G25 I don't know.

Please do!

[Anglesqueville]

Published: 10 January 2024
Population genomics of post-glacial western Eurasia
... we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. ...
https://doi.org/10.1038/s41586-023-06865-0

Sorry if obvious to others, but is all raw data (except the 100 Danish genomes?) already public since months including in Eurogenes G25 values or has some still to be published (now with the official article)?

https://erda.ku.dk/archives/917f1ac64148...chive.html

If necessary I can provide an eigenstrat file reduced to 1240K with the usual codings. For G25 I don't know.

Please do!

https://www.dropbox.com/scl/fo/9v0qcm1dk...i3zdy&dl=0

edit: I'm seemingly out of space on my dropbox. I believe the files have been uploaded (>2Gb), but tell me if there are problems.

[Kale]

edit: I'm seemingly out of space on my dropbox. I believe the files have been uploaded (>2Gb), but tell me if there are problems.

Worked for me! Thank you sir

I assume the second half of the dataset is the imputed versions? The samples with _rnd appended to the end?

[teepean]

Published: 10 January 2024
Population genomics of post-glacial western Eurasia
... we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. ...
https://doi.org/10.1038/s41586-023-06865-0

Sorry if obvious to others, but is all raw data (except the 100 Danish genomes?) already public since months including in Eurogenes G25 values or has some still to be published (now with the official article)?

https://erda.ku.dk/archives/917f1ac64148...chive.html

If necessary I can provide an eigenstrat file reduced to 1240K with the usual codings. For G25 I don't know.

Please do!

https://www.dropbox.com/scl/fo/9v0qcm1dk...i3zdy&dl=0

edit: I'm seemingly out of space on my dropbox. I believe the files have been uploaded (>2Gb), but tell me if there are problems.

Conversion to plink succeeded so I assume the upload was succesful.

[Anglesqueville]

edit: I'm seemingly out of space on my dropbox. I believe the files have been uploaded (>2Gb), but tell me if there are problems.

Worked for me! Thank you sir

I assume the second half of the dataset is the imputed versions? The samples with _rnd appended to the end?

Yes, the _rnd samples are the non-imputed ones. I've already worked a little with the imputed genomes (reduced to 1240K), in particular with the Swedes from Falköping. They have done a pretty great job.

[Uintah106]

NEO261; 2112-1778 BC; Sillvik, Sweden; LNBA; I1a-DF29>Z2893 (Z63,Z58,FGC15556,A5741,Y14628,Y11204,FTB21048,PH790,BY169148)


NEO93; 1886-1689 BC; Stroby Ladeplands, Denmark; Bronze Age; I1a2a1-Z58 (xZ138,CTS8647,Z2041,A12798,Y128537,A22488)

Can you please look at  NEO83 if its yet available ?

The files are there if that's the question.

Great. The follow-up is if anyone can have a look at the sub-clades below 'R1b'

Could anyone take a look at these six  Danish Neolithic samples:NEO870,NEO872,NEO92,NEO737,NEO860 and NEO735. Would be much appreciated !