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Thread: PLINK extracting to 23&Me format - too large size of file

  1. #11
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    a couple of minutes longer to annotate the VCF with dbSNP
    ... rather a couple of couples of minutes, if Pagani has written one vcf per chrom, as he did with the beds. . I guess that Pagani did'nt imagine that somebody could have the need to make 23&me files of individuals extracted from his basis. Personally my only problem was to merge my father with Pagani, and of course I remade the annotation of my father's file, not of Pagani!
    Last edited by anglesqueville; 10-11-2017 at 07:58 AM. Reason: spelling!!!
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     khanabadoshi (10-11-2017)

  3. #12
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    Quote Originally Posted by anglesqueville View Post
    .. I guess that Pagani did'nt imagine that somebody could have the need to make 23&me files of individuals extracted from his basis.
    Yes, my reason was to extract three Aeta kits. Out of curiosity. To check if they have Phillipino relatives on Gedmatch and how many, and of course how they behave in various calculators.
    What is strange with that?

    @Kurd
    Perhaps he only wanted serious people to use his data
    I don't know if my above reasons are serious or not. I learned PLINK just one week ago and extracted all samples from all public datasets (which were in PLINK format) except Pagani
    All are uploaded on Gedmatch now, but hidden under "Research" label... I don't want to dominate some one-to-many results completely with them (like SE-Asia or Central Asia).
    Last edited by lukaszM; 10-11-2017 at 12:29 PM.

  4. #13
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    Lukasz:
    What is strange with that?
    Strictly speaking, nothing. I just think that Pr Pagani was just ( and is still) unable to imagine that somebody could use his datas in this way. That said, those datas are public, and you are allowed to use them as you want.

    edit: honnestly the ways I used myself Pagani ( 2 times only) can seem themselves strange, or at least highly adventurous. In particular the work I did on the HLA with the Uralics from Pagani, my father (imputed), and diverse admixtools programs was likely on the fringes of what is reasonable.

    edit edit: Lukasz, as you are always looking for modern individuals, did you try with Simon Genome Diversity Project? ( link on Reich' page at Harvard)
    Last edited by anglesqueville; 10-11-2017 at 12:50 PM.
    En North alom, de North venom
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    (Roman de Rou, Wace, 1160-1170)

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    Quote Originally Posted by anglesqueville View Post
    Lukasz: Strictly speaking, nothing. I just think that Pr Pagani was just ( and is still) unable to imagine that somebody could use his datas in this way. That said, those datas are public, and you are allowed to use them as you want.
    Yes it's possible that he can't

    I like complete solutions and it makes me sick that I can't use Pagani (yet...).
    If something interests me I must gather all possible info
    Last edited by lukaszM; 10-11-2017 at 12:53 PM.

  7. #15
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    Quote Originally Posted by lukaszM View Post
    Yes it's possible that he can't

    I like complete solutions and it makes me sick that I can't use Pagani (yet...).
    If something interests me I must gather all possible info
    I can put the plinks of the Aeta samples on google drive for you if you like and Annotate RS numbers With HG 19 reference?
    EurasianDNA.com - A study of the population history of West & South Asia.

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     anglesqueville (10-11-2017)

  9. #16
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    Quote Originally Posted by Kurd View Post
    I can put the plinks of the Aeta samples on google drive for you if you like and Annotate RS numbers With HG 19 reference?
    Ok if you can, would be great.

  10. #17
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    Quote Originally Posted by lukaszM View Post
    Ok if you can, would be great.
    Here you go in Plink format. I also included the 3 Agta samples. All mapped to hg19 with dbSNP nos, with X chr, and about 900K SNPs. I removed no calls.

    https://drive.google.com/file/d/0B5L...ew?usp=sharing
    EurasianDNA.com - A study of the population history of West & South Asia.

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     anglesqueville (10-11-2017), khanabadoshi (10-11-2017), lukaszM (10-11-2017)

  12. #18
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    Quote Originally Posted by Kurd View Post
    Here you go in Plink format. I also included the 3 Agta samples. All mapped to hg19 with dbSNP nos, with X chr, and about 900K SNPs. I removed no calls.

    https://drive.google.com/file/d/0B5L...ew?usp=sharing
    Thanks!

    Still I will be trying to manage it by yourself. I have some idea with --extract use but I must test.

  13. #19
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    Thanks to R solution provided by Anglesqueville by PM I converted to 23&me format finally whole Pagani dataset

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