Add 2024_Penske_Leubingen

[stschiff]

PR Checklist for a new package submission

• The package does not exist already in the community archive, also not with a different name.
• The package title in the POSEIDON.yml conforms to the general title structure suggested here: <Year>_<Last name of first author>_<Region, time period or special feature of the paper>, e.g. 2021_Zegarac_SoutheasternEurope, 2021_SeguinOrlando_BellBeaker or 2021_Kivisild_MedievalEstonia.
• The package is stored in a directory that is named like the package title.

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• The package is complete and features the following elements:
  • Genotype data in binary PLINK format (not EIGENSTRAT format).
  • A POSEIDON.yml file with not just the file-referencing fields, but also the following meta-information fields present and filled: poseidonVersion, title, description, contributor, packageVersion, lastModified (see here for their definition)
  • A reasonably filled .janno file (for a list of available fields look here and here for more detailed documentation about them).
  • A .bib file with the necessary literature references for each sample in the .janno file.
• Every file in the submission is correctly referenced in the POSEIDON.yml file and there are no additional, supplementary files in the submission that are not documented there.
• Genotype data, .janno and .bib file are all named after the package title and only differ in the file extension.
• The package version in the POSEIDON.yml file is 1.0.0.
• The poseidonVersion of the package in the POSEIDON.yml file is set to the latest version of the Poseidon schema.
• The POSEIDON.yml file contains the corresponding checksums for the fields genoFile, snpFile, indFile, jannoFile and bibFile.
• There is either no CHANGELOG file or one with a single entry for version 1.0.0.

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• The Publication column in the .janno file is filled and the respective .bib file has complete entries for the listed mentioned keys.
• The .janno file does not include any empty columns or columns only filled with n/a.
• The order of columns in the .janno file adheres to the standard order as defined in the Poseidon schema here.
• The .janno and the .ssf files are not fully quoted, so they only use single- or double quotes ("...", '...') to enclose text fields where it is strictly necessary (i.e. their entry includes a TAB).

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• The package passes a validation with trident validate --fullGeno.

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• Large genotype data files are properly tracked with Git LFS and not directly pushed to the repository. For an instruction on how to set up Git LFS please look here. If you accidentally pushed the files the wrong way you can fix it with git lfs migrate import --no-rewrite path/to/file.bed (see here).

[stschiff]

OK, so @SandraPenske has kindly (and heroically) filled the Janno file, including all these many many relationships! I have just added the genotype data to which Sandra pointed me. I think this is ready for review.

[nevrome]

@wolfgangaroo Could I ask you to quickly look through this package -- specifically through the .janno, the .bib and the POSEIDON.yml file? I assigned you as a reviewer, but feel free to decline.

[TCLamnidis]

Quick note about the Damage column. You have values between 0 and 1, yet acccording to the janno specification This should range from 0-100.

The Damage column contains the % damage on the first position of the 5’ end for the main Shotgun library used for sequencing or capture. This is an important statistic to verify the age of ancient DNA. In case of multiple libraries you should report a value from the merged read alignment.

I think the values then need to be multiplied by 100?

I think this is an issue that is actually quite prevalent across our archives. Might be worth a batch update? Or update the schema.

P.S. Actually, I think that's also the case for Endogenous, even though in most cases we report it as a 0-1 range.

[SandraPenske]

Hey Thiseas, You are correct! The values have to be multiplied by 100! They were basically just copied and pasted out of the eager output! Thiseas C. Lamnidis ***@***.***> schrieb am Mi., 12. Feb. 2025, 01:37:

…

Quick note about the Damage column. You have values between 0 and 1, yet acccording to the janno specification This should range from 0-100. The Damage column contains the % damage on the first position of the 5’ end for the main Shotgun library used for sequencing or capture. This is an important statistic to verify the age of ancient DNA. In case of multiple libraries you should report a value from the merged read alignment. I think the values then need to be multiplied by 100? I think this is an issue that is actually quite prevalent across our archives. Might be worth a batch update? — Reply to this email directly, view it on GitHub <#244 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BKRS3ILRWQSKWEVZDEREXPD2PIG2HAVCNFSM6AAAAABWMF4FPSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNJRGA4TQMBZGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[stschiff]

OK good catch. I will rescale them.