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  • Apr 19 10:49

    tsujigiri on refactor-zip_genotyping_files

    (compare)

  • Apr 19 10:49

    tsujigiri on master

    Refactor ZipGenotypingFiles (#5… (compare)

  • Apr 19 10:49
    tsujigiri closed #527
  • Apr 19 09:51
    tsujigiri synchronize #527
  • Apr 19 09:51

    tsujigiri on refactor-zip_genotyping_files

    Just details (compare)

  • Apr 18 17:23
    tsujigiri synchronize #527
  • Apr 18 17:23

    tsujigiri on refactor-zip_genotyping_files

    Make Rubocop happy (compare)

  • Apr 18 17:10
    tsujigiri opened #527
  • Apr 18 17:10
    Travis openSNP/snpr (refactor-zip_genotyping_files) passed (2292)
  • Apr 18 17:07

    tsujigiri on refactor-zip_genotyping_files

    Fix factory formatting Add test for Zipgenotypingfiles… Refactor Zipgenotypingfiles and 1 more (compare)

  • Apr 18 11:38
    tsujigiri opened #526
  • Feb 28 20:38
    Travis openSNP/snpr@31eaaec (dependabot/bundler/rake-13.0.1) passed (2290)
  • Feb 28 20:36
    dependabot[bot] labeled #525
  • Feb 28 20:36
    dependabot[bot] opened #525
  • Feb 28 20:36

    dependabot[bot] on bundler

    Bump rake from 12.3.1 to 13.0.1… (compare)

  • Feb 27 08:29
    Travis openSNP/snpr@9351549 (dependabot/bundler/rack-1.6.13) passed (2288)
  • Feb 27 08:25

    dependabot[bot] on bundler

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  • Feb 27 08:25
    dependabot[bot] closed #522
  • Feb 27 08:25
    dependabot[bot] commented #522
  • Feb 27 08:25
    dependabot[bot] labeled #524
philiprhoades
@philiprhoades
Philipp and Bastian,
Right - thanks for that.
Bastian Greshake Tzovaras
@gedankenstuecke
MyHeritage is pretty big these days too and my best guess is that it doesn’t really make a big difference which provider you go with as the data is pretty similar across all of them
philiprhoades
@philiprhoades
Right - good to know.
Bastian Greshake Tzovaras
@gedankenstuecke
I know that MyHeritage allows the upload of data from other providers
I’m not sure whether Ancestry allows that too
Philipp Bayer
@philippbayer
probably not from looking through their faq, no mentinos
philiprhoades
@philiprhoades
Yes, I just tested that as an exercise with MyHeritage - it took them a few days to process the 23andMe file and I got a bit of info back but to get all of the info they want to charge another AUS$48 . .
It looks like we might stick with 23andMe just for the convenience of most of the family already being there . .
Bastian Greshake Tzovaras
@gedankenstuecke
yeah, that certainly makes things easier if you already have many people on 23andme
Philipp Bayer
@philippbayer
makes sense to me!
Bastian Greshake Tzovaras
@gedankenstuecke
and i just uploaded my own 23andme data to myheritage just for fun, to see what they offer :)
philiprhoades
@philiprhoades

I know what you mean about scaling and processing but for some years I have been following:

https://safenetwork.org

which could potentially offer a distributed store of data and possibly processing . . it would be great to have an inexpensive store and comparison of nearly ALL the data from the commercials . .

Philipp Bayer
@philippbayer
currently we're still ok (thanks to patreon!!) but it could be a thing for the future!
philiprhoades
@philiprhoades
There is a bunch of stuff I want to put there once they go live - I will keep this stuff in mind and bring it up again in the future . .
Bastian Greshake Tzovaras
@gedankenstuecke
thanks!
Philipp Bayer
@philippbayer
Bastian Greshake Tzovaras
@gedankenstuecke
wow!
Bastian Greshake Tzovaras
@gedankenstuecke
420 and me! :D
Philipp Bayer
@philippbayer
I didn't see that dna.land is closing down/relaunching as a commercial service? https://medium.com/@dl1dl1/dna-land-is-relaunching-34f5a505504f
Philipp Bayer
@philippbayer
I like this: 'Please note that because DNA.Land is closing as a research project, all accounts and data will be permanently deleted and erased from the DNA.Land servers on September 30th, 2019. You will be able to recreate an account on DNA.Land 2.0 and upload your data just as you did when you signed up to join DNA.Land.'
Bastian Greshake Tzovaras
@gedankenstuecke
@philippbayer yeah, that’s cool. I had missed that somehow!
Philipp Bayer
@philippbayer
updating ssl certificate right now, server seems to have trouble coming back
oh. the harddrive is full\
Philipp Bayer
@philippbayer
ok fixed, for now
Bastian Greshake Tzovaras
@gedankenstuecke
whops :D
i think our automated cleanup of older zip archives doesn’t work, that’s why it just keeps adding them :D
Paweł Olszewski
@olszewskip
Hi, hello!
I'm interested in doing some genome-wide, "population-long" association studies between genotypes and phenotypes, with the motivation being just self-education and training in this sort of analyses, trying out different statistics and algorithms etc. First I was planning on simulating data with HAPGEN2, but then I stumbled upon openSNP. I was wondering if You know of any existing projects that use openSNP data for discovering phenotype associations? Also, maybe You can recommend any software tools for converting the genotypes from openSNP into a uniform file format, like VCF?
Bastian Greshake Tzovaras
@gedankenstuecke

hey @olszewskip! There was one crowdsourced AI challenge done with the data that would fit your description: https://www.crowdai.org/challenges/opensnp-height-prediction

They also created an open source pipeline to prepare the data from openSNP for the challenge: https://github.com/onaret/opensnp-cohort-maker

Paweł Olszewski
@olszewskip
Awesome! Many thanks.
Bastian Greshake Tzovaras
@gedankenstuecke
And if you want to use plink for the GWAS: They actually have a function to convert 23andMe files to the input plink needs
Paweł Olszewski
@olszewskip
Nice, I was vaguely aware of that, but I haven't yet had a chance of working with any 23andMe files. Does it make sense to use plink not only for GWAS'es but also simply for 23andMe -> VCF conversion?
Bastian Greshake Tzovaras
@gedankenstuecke
iirc plink doesn’t use VCF files but their own, more simple format. I think @philippbayer knows more about that though
Paweł Olszewski
@olszewskip
Sadly I cannot access the data prepared by crowdai without an account, and I cannot sign up because apparently the site is shutting down and not allowing new sign-ups :( If anyone knows of any way that I could still access that AI challenge data, please let me know.
Bastian Greshake Tzovaras
@gedankenstuecke
I’d try emailing them if there’s a contact email
@olszewskip if there’s no email around let me know and i’ll look through my archives and find it
Paweł Olszewski
@olszewskip
Sylvain Bernard from EPFL has kindly provided me with the data. Many thanks, @gedankenstuecke
Bastian Greshake Tzovaras
@gedankenstuecke
yay, that’s great! :)
alcogni
@alcogni
@gedankenstuecke I downloaded some phenotypes and genotypes included sometimes belongs to users either not at openSNP website anymore or the user number at website and user number at genotype are different. Could you please help me to understand.
JialinKang
@JialinKang
hi, the website opensnp.org is broke.
Helge Rausch
@tsujigiri
Oops... You are right! 🔎
Bastian Greshake Tzovaras
@gedankenstuecke
@JialinKang thanks to @tsujigiri the site is back up 💖
marcushdawson
@marcushdawson
Hi, I am getting "404: Whatever you tried to access is not here." message when trying to download all data from OpenSnp
Bastian Greshake Tzovaras
@gedankenstuecke
hey @marcushdawson, thanks for letting us now! I think there was an issue with creating the latest version of the archive and I’ve already kicked the machine and restarted the job. So hopefully at the end of the day there should be a new one :)
marcushdawson
@marcushdawson
Ok awesome, thanks for the quick response @gedankenstuecke. I hope the kicking works!
Bastian Greshake Tzovaras
@gedankenstuecke
yeah, the task is already 3 hours in, but it usually takes around half a day to create the archive i think
Sina Rüeger
@sinarueeger
Hi! The SSL certificate for opensnp.org seems to have expired recently (5/20/2020). Could you have a look?
Bastian Greshake Tzovaras
@gedankenstuecke
thanks @sinarueeger, doing the update right now :)
and fixed :)
Sina Rüeger
@sinarueeger
Thanks @gedankenstuecke for the quick fix!