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choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis
MIT License
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PRS on UK Biobank data #4

Open jielab opened 4 years ago

jielab commented 4 years ago

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 commented 4 years ago

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

On Sat, Jun 27, 2020 at 11:42 PM jiehuang001 notifications@github.com 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

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