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Thread: New K12 Ancient Calculator

  1. #21
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    Quote Originally Posted by Dibran View Post
    Awesome. Does this auto update for those who purchased the previous version? Or do funds have to be submitted again? Additionally, are the recent Mycenaean samples factored in?

    Best regards.
    Yes, that's what I had proposed to Geneplaza, and they were ok with it, but I'll discuss this again with them tomorrow. The Mycenean samples were not included but its possible that they may be added later.

    Also, some may be aware that I have been busy trying to develop a pipeline for diploid processing aDNA over the past month, since the overwhelming majority of aDNA sequences released by Harvard and other institutions are haploid, and thus are limited in accuracy, and don't do very well in IBD comparisons. After butchering Broad Institute's GATK workflow, and adding my own experimental steps, things look promising and I have a few diploid sequences processed using different scenarios. As soon as I'm done with QC I will gradually stary incorporating them as well.
    EurasianDNA.com - A study of the population history of West & South Asia.

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  3. #22
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    Quote Originally Posted by noman View Post
    Wow! This is so cool. Would try it.
    Question: don't you think ancestry calculator at geneplaza needs some changes? I mean, it shows a very high percentage of Central Asia for me, and I am not even Central Asian.

    Besides knowing that it's a structure based program developed by Joe Pickerell, a well respected geneticist, I don't know much about it, and don't have any input into it.

    If you get high C Asian, that indicated to me that the S Asian references are very southern Indians. Comversely, if the S Asian references would have been N Indians, then I would expect a cheer central Asian score would be much lower
    EurasianDNA.com - A study of the population history of West & South Asia.

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  5. #23
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    Quote Originally Posted by Kurd View Post
    UPDATE:

    The K12 Ancient calculator should be live by Sunday absent any unanticipated issues

    [IMG][/IMG]
    [IMG][/IMG]


    Edit: Just noticed a mistyped pop label. Should be West European and Scandinavian hunter gatherers

    Also, Andronovo should be Andronovo-Srubnaya




    UPDATE

    I had to diagnose and resolve a technical issue with the production version at GenePlaza. So it looks like the calculator should be live by Wednesday. Also, I confirmed that K11 customers will be updated with the K12 at no charge.
    EurasianDNA.com - A study of the population history of West & South Asia.

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  7. #24
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    Quote Originally Posted by Kurd View Post
    UPDATE

    I had to diagnose and resolve a technical issue with the production version at GenePlaza. So it looks like the calculator should be live by Wednesday. Also, I confirmed that K11 customers will be updated with the K12 at no charge.
    Great; thank you!
    Kashmir

  8. #25
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    kurd kudos,
    can you add Ehg samples
    to the k12 ?

    kind regards
    adam
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  9. #26
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    Quote Originally Posted by kingjohn View Post
    kurd kudos,
    can you add Ehg samples
    to the k12 ?

    kind regards
    adam
    There is only one decent EHG sample out there, not enough to form a reliable component, although the EHG sample is one of the steppe samples I am currently diploid processing. I will make it available in diploid with transition and transversion bases as well as a diploid transversions only version, along with some other steppe samples within two weeks, so that they can be used for IBD and formal stats .
    EurasianDNA.com - A study of the population history of West & South Asia.

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  11. #27
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    Quote Originally Posted by Kurd View Post
    Yes, that's what I had proposed to Geneplaza, and they were ok with it, but I'll discuss this again with them tomorrow. The Mycenean samples were not included but its possible that they may be added later.

    Also, some may be aware that I have been busy trying to develop a pipeline for diploid processing aDNA over the past month, since the overwhelming majority of aDNA sequences released by Harvard and other institutions are haploid, and thus are limited in accuracy, and don't do very well in IBD comparisons. After butchering Broad Institute's GATK workflow, and adding my own experimental steps, things look promising and I have a few diploid sequences processed using different scenarios. As soon as I'm done with QC I will gradually stary incorporating them as well.
    Thats awesome. Incorporating them in the geneplaza calc or making new alternate calculators? Thank you for all the hard work you do!
    Known Ancestry: Albanian
    23andme results: 94% Balkan, 0.9% Italian, 0.8% Middle Eastern, 2.2% broadly southern European, 0.3 British & Irish, 0.3% Japanese, 0.5% unassigned
    MyOrigins2.0: 100% Southeast European
    MyAncientOrigins: 62% Farmer, 24% Hunter Gatherer, 14% Metal Age Invader
    MyHeritage: 76% Greek, 16% Balkan, 8% Italian
    WeGene: 99.5% Balkan, 0.5% unassigned
    GenePlaza: 92.7% East Mediterranean, 5.2% Southwestern European, 1.5% Ambiguous
    DNA.LAND: 95% Balkan, 5% Sardinian

  12. #28
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    Quote Originally Posted by Dibran View Post
    Thats awesome. Incorporating them in the geneplaza calc or making new alternate calculators? Thank you for all the hard work you do!
    Haven't decided yet.
    EurasianDNA.com - A study of the population history of West & South Asia.

  13. #29
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    There will be no Northeast Asian component in this new calculator?

  14. #30
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    Quote Originally Posted by Kylo_Ren View Post
    There will be no Northeast Asian component in this new calculator?

    No, since I'm trying to utilize ancient populations as much as possible, and most E Asian DNA in W Eurasians was conferred by ancient populations, either substantially descended from, or partially descended from,and/ or related to, Karasuk and E Scythian types, instead of directly via interactions with NE Asian moderns.

    In addition to being more consistent with reality (for W Eurasians) than NE Asian moderns, the use of Karasuk and E Scythians ancients gives us the added benefit of being able to gauge what percentage Karasuk/E Scythian input is necessary to elevate a W Eurasian's NE Asian admixture to 2,3,4 or whatever percentage

    unfortunately, we as of yet don't have a collection of NE Asian aDNA, therefore, this calculator may not adequately describe demography for NE Asians
    Last edited by Kurd; 08-27-2017 at 03:45 PM. Reason: Added NE Asian moderns
    EurasianDNA.com - A study of the population history of West & South Asia.

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