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openSNP/snpr

The sources of the openSNP website

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Mar 14 15:34

gedankenstuecke closed #537
Mar 14 15:34

gedankenstuecke commented #537
Mar 14 10:00

joannearcilla opened #537
Feb 06 14:35

tsujigiri synchronize #536
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Update paperclip gem (compare)
Feb 05 16:46

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Feb 05 16:41

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Feb 05 16:28

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Feb 05 16:04

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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!

Amborella

@Amborella

Hi! I'm new here and not an expert on genetics but if you look at the page for SNP rs187238 it says the genotype frequency for CC is 54%, CG is 39% and GG is 7%. However the article this info is based on here seems to say that GG has frequency 54% and CC has frequency 7%. Am I misinterpreting something or is it the wrong way around on the website? Thanks!

Bastian Greshake Tzovaras

@gedankenstuecke

hey @Amborella! That’s well spotted. This is most likely the result of how 23andMe reports their SNPs. 23andMe and most other genotyping companies report the variations all based on the +/forward strand of the DNA. But dbSNP and many publications etc. give variants based on the orientation of the gene.

In the case you highlight the IL18 gene is on the -/reverse strand of the DNA (see https://www.snpedia.com/index.php/Rs187238), so one needs to take the complement of the reported 23andMe allele to be in line with that notation, which flips the Gs & Cs around in this case.

Hope that makes sense! :)

Amborella

@Amborella

Hi Bastian! Thanks for the quick reply. I sort of understand what you are talking about. Just to confirm if I took a genetic test and got CC as my genotype what would it correspond to in openSNP? Thanks!

Also according to what it says on openSNP 7% of the population (those with genotype GG by the notation on the page) have increased risk for SCD due to hypertension while according to the original paper 54% of people had this risk (those with genotype GG going by the notation in the original paper). Should the complement be taken somewhere here as well?

Bastian Greshake Tzovaras

@gedankenstuecke

in openSNP it will also be noted down as CC. But if you look at dbSNP, SNPedia or any other source that takes orientation into account you need to check if the variant of interest is on the minus strand

So if you are CC in 23andme (and by extension in openSNP), then this translates to being GG in the paper you are looking at

and then i think all the numberes make sense, no? 7% CC in openSNP means we have 7% GG in the notation of the paper?

Amborella

@Amborella

Thanks for the reply. If you look at the Links to SNPedia bit on the page it says: "rs187238 G/G Hypertension increases risk 3.75x for sudden cardiac death". On openSNP it says 7% of people have this genotype while the paper says 54% do.

From your reply I get the impression that it is not possible to just go from the genotype frequency on openSNP to the Links to SNPedia to work out what percentage of population is susceptible to the increased risk without checking if the variant is on the negative strand. Can you confirm if that is correct?

Bastian Greshake Tzovaras

@gedankenstuecke

yes, and the snpedia page gives that informatio

so for rs187238 SNPedia says that GG on the minus strand gives the elevated risk, which the paper says is found in 54% of the population. As it’s on the minus strand we have to look at the CC in openSNP and can see that 54% of openSNP members have that variant too, no?

Amborella

@Amborella

Great, thanks a lot. That makes it much clearer!

Also as an aside how do you tell if a SNP is on the negative strand from SNPedia? Is it the - in -137G or something else?

Bastian Greshake Tzovaras

@gedankenstuecke

in the box on the right hand side the first item is “orientation minus"

Amborella

@Amborella

Got it. Thanks!

Philipp Bayer

@philippbayer

nice, i just resubmitted a paper on Amborella pangenomics

Amborella

@Amborella

Yeah, I think Amborella is amazing. Strongly considering taking a holiday in New Caledonia sometime in the next few years just so I can get myself a pot of the stuff and bring it back. Although I'm more interested in it from the rare plant side of things than the genetics side.

Bastian Greshake Tzovaras

@gedankenstuecke

All the best for the resubmission!

Sina Rüeger

@sinarueeger

Hi, for some reason the SSL certificate expired again, could you update that?

Philipp Bayer

@philippbayer

sorry about that, fixing it right now

done!

Sina Rüeger

@sinarueeger

many thanks!

Philipp Bayer

@philippbayer

@gedankenstuecke @tsujigiri i've just added a bash script to /root/run-letsencrypt.sh and added that to crontab, let's see whether that works :PP

the current cert expires Sunday, 22 November 2020. if it works right then next thursday (tomrorow) we'll have a later cert.

Helge Rausch

@tsujigiri

I already added a CRON job earlier. Doesn't seem to work... :laughing:

Helge Rausch

@tsujigiri

0 0 * * * root /usr/local/bin/renew_ssl_cert.sh

Bastian Greshake Tzovaras

@gedankenstuecke

😂

Is it because something needs to be run as app instead of root for the containers?

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