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Thread: Online Pigmentation Predictor

  1. #121
    Registered Users

    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 4 Users Say Thank You to Sangarius For This Useful Post:

     Kurd (12-06-2017), Lank (12-06-2017), poi (01-07-2018), Varun R (12-06-2017)

  3. #122
    Registered Users

    Spain Poland
    I used the DNA.LAND imputed data to complete the 23andme V5 file SNPs that I got, and I carried out the test.
    I had to change two SNPs alleles to the ones proposed by the tool.
    I think is pretty accurated, even using 30% SNPs from imputed data.



  4. The Following User Says Thank You to wilhelmhalys For This Useful Post:

     Kurd (02-10-2018)

  5. #123
    Registered Users

    Can anyone make sure I did this correctly (using my FTDNA.b37 and 23andme.V5 data):

    SNP-Indels	ftdna	v5	combo	final
    rs10777129	GG	-	GG	GG
    rs13289		-	-	-	NN
    rs1408799	-	TT	TT	GG
    rs1426654	AA	AA	AA	AA
    rs1448484	-	-	-	NN
    rs16891982	-	CG	CG	CG
    rs2402130	AA	-	AA	AA
    rs3829241	AG	-	AG	CT
    rs6058017	-	-	-	NN
    rs6119471	-	-	-	NN
    Did I do this right? I am seeing weird results, so want to confirm before using imputed alleles to fill the NNs.
    Last edited by poi; 02-19-2018 at 10:27 PM. Reason: typo

  6. The Following User Says Thank You to poi For This Useful Post:

     bmoney (02-20-2018)

  7. #124
    Registered Users
    North Florida

    United States of America Spain Basque Italy Portugal Cuba
    Let me go ahead an make a Public Service Announcement PSA:

    In the above calculator rs16891982 is backwards (notice it says reverse in the website). That means that if you are GG you should enter CC; notice that the allele frequency in the parent populations are backwards with C being solely found in 84% of White; and G being found in the majority of Intermediate and all(95%) of the Black. Go ahead a correct this to get appropriate results. If you are heterozygous then is ok; but be mindful of the allele frequencies.

  8. The Following User Says Thank You to jeanL For This Useful Post:

     bmoney (02-20-2018)

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