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Thread: Online Pigmentation Predictor

  1. #121
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    Update: In order to fill-in the missing markers I downloaded's imputed VCF files. I did this for my own and my grandparents kits.

    Some notes on's imputed VCF files:
    I hadn't bothered with's imputed VCF until now, as it seemed kinda daunting and mysterious to me.
    But now that I engaged a little bit with the topic of imputation, I believe this to be the single best service offering for genomics enthusiasts out there. Either I'm missing something, or this really is a highly underappreciated service offering.

    Compared to all other "genomics service platforms" that are popping up left and right (decoying users with shitty admixture runs in return for their valuable kits), users really get something of incredible value that they don't get anywhere else. About 40 million imputed SNPs with an accuracy of 99.994%. While not optimal for mendelian traits, this is excellent for the really interesting highly polygenic traits concerning health, cognition, physique etc. that are targeted by GWAS studies. For example the 36 SNP skin color predictor that Kurd is working on (based on Walsh et al. 2017 ?) is exactly the kind of model that the imputed VCF file is perfectly suited for. The more SNPs used by a model the less of a concern the imperfect accuracy becomes.

    While I had uploaded my own and my maternal grandparents kits already in 2015, I only uploaded my paternal grandparents kits a couple days ago. Thereby I noticed a couple of things:
    - the imputed VCF files of my paternal grandparents don't have the ending ".vcf.gz", but only ".vcf". But they are not VCF files, if you try to open them with glogg you will get corrupted output. You actually have to add ".gz" to the file ending. Then it's possible to unpack them or use with's compass.
    - my paternal grandparents files are about 0.5gb smaller than the our VCF files and show missing markers when using with's compass.
    - when opening the new VCF files with glogg, the format looks different than the old files. While quite a lot smaller in size, the new VCF files have 6 million (!) more SNPs (43.8M vs 37.8M SNPs).
    - The reason: my paternal grandparents VCF files are in the newer VCF v4.1 format, while our older VCF files are in v4.0 format.
    I wonder how new this change to v4.1 is, considering that hasn`t updated their website nor their compass application. I had to do quite a bit of google research to understand how to interpret the new imputation probabilities. (v4.0 format: 0/0:0.00,-10.00,-10.00 ; v4.1 format: 0|0:0 )

    Pigmentation results:
    My maternal grandma comes out as lightest, closely followed by my maternal grandpa. After a large gap my paternal grandma and grandpa follow. This doesn't really map onto reality, though. While all of my grandparents are definitely white in terms of coloration, the order isn't correct. It seems like the rather high East-Eurasian admixture that my paternal grandparents have (>15%) influences their results. The calculator is primed on white vs black and doesn't consider (North)-East-Eurasian variation. I wonder how a light East-Eurasian individual would score on this calculator. Anyway, looking forward to Kurd's 36 SNP calculator.


    Mine (23andme v3)





  2. The Following 3 Users Say Thank You to Sangarius For This Useful Post:

     Kurd (12-06-2017), Lank (12-06-2017), Varun R (12-06-2017)

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