PRS on UK Biobank data

[jielab]

Hi, It would be very nice to add a guide on LDpred-funct, and SbayesR, which are popular as well.

Also, it would be good to show how to generate PRS for UKB data (500,000 samples) with millions of SNPs. This seems to be a trend now.

Best regards,
Jie

[choishingwan]

I agree with you. Unfortunately, I don't currently have the time required for me to code those up (and I might also need to update LDpred tutorial to LDpred2) so that is unlikely to happen anytime soon. You are more than welcome to help us write up a tutorial for those tools though. (don't think codes for the latest LDpred-funct is available yet) As for UK Biobank data, at least for PRSice and lassosum, you should be able to run those scripts on the UK Biobank data just fine. Even the QC steps should more or less translate to UK biobank data (with the exception of maybe relatedness calculation). If you want scripts on UK Biobank QC, you can find it here <https://gitlab.com/choishingwan/uk-biobank-piplines> Regards, Sam

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On Sat, Jun 27, 2020 at 11:42 PM jiehuang001 ***@***.***> wrote: Hi, It would be very nice to add a guide on LDpred-funct, and SbayesR, which are popular as well. Also, it would be good to show how to generate PRS for UKB data (500,000 samples) with millions of SNPs. This seems to be a trend now. Best regards, Jie — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYQY7KA2YWU5D6K2UBDRYYHPFANCNFSM4OKCTJGQ> .