Create 2023_Rodriguez_Varela.janno

[Helsinki-Ronan]

.janno file for future use.

Rodríguez-Varela et al. 2023	Cell	The genetic history of Scandinavia from the Roman Iron Age to the present	2023	https://doi.org/10.1016/j.cell.2022.11.024

[nevrome]

Thanks for preparing this .janno file! I see the following issues

• The package name does not follow our expected standard of Year_AuthorName_RelevantKeyword. I propose 2023_RodriguezVarela_Scandinavia.
• Please remove all columns that are completely empty/filled only with n/a.
• The Genetic_Sex must be one of F, M or U.
• If Contamination and Contamination_Err are empty then Contamination_Meas must be empty as well.
• Date_Type must be C14, not c14.
• If Date_Type == C14, then Date_C14_Uncal_BP and Date_C14_Uncal_BP_Err can not be empty.
• The Source_Tissue ancient_human_skeletal_element is not very informative. If the paper does not specify further, e.g. by distinguishing bone or teeth, then I suggest to leave the column empty and remove it.
• The note reads Data are a mix of UDG-treated and untreated libraries. Cannot find information as to which libraries are UDG-half or UDG-full Setting udg to “minus”. @TCLamnidis

Maybe you could quickly have a look 👍. Please run trident validate --janno on the file after you implemented the necessary changes.

[TCLamnidis]

I renamed the janno file, but cannot rename the directory on GH. @Helsinki-Ronan , maybe you could rename the directory on your fork to 2023_RodriguezVarela_Scandinavia?

[stschiff]

@Helsinki-Ronan could you perhaps reach out to Anders or the first author of this paper and ask them for the genotype data for this package? We would like author-made genotype data for this repository, not the one from AADR. Thanks!

[Helsinki-Ronan]

@TCLamnidis I just synced my fork with yours (Poseidon's) and the package appears as 2023_RodriguezVarela_Scandinavia so I guess you renamed it yourself?

@stschiff I'm not sure what you mean. The data is from ENA, not from AADR. Or do they both point to the same thing?

[TCLamnidis]

@Helsinki-Ronan The files I could rename, but not the directory

[stschiff]

OK, so what I meant was: In order to elevate this Janno-file, which you kindly prepared, to a package, we need Genotype data. Either we transfer this Janno over to Minotaur and generate it ourselves from the raw data on ENA, or we ask the original authors to share 1240K genotype with us. Both is possible, we just need to decide. I thought that perhaps it's worth a shot to reach out to Anders Götherström and the first author and ask them. I'm happy to do so myself, shoud I, or would you want to try, @Helsinki-Ronan? I'm just asking because you are the current assignee for this package so you can decide.

[TCLamnidis]

this package has a minotaur archive PR pending, and the provided janno was used there already (and even supplemented).
Getting genotypes from the first authors would be best, but failing that, the information here is already making its way to the PMA