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rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
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Question about prediction in Step 1 #526

Closed Youpu-Chen closed 4 months ago

Youpu-Chen commented 5 months ago

Hi there.

According to the UKBB tutorial, I was a little bit confused.

Can I build the Step 1 prediction model for each chromosome (and run Step 2 for each chromosome using the chromosome-level Step 1 results), instead of using the whole genome PLINK bed file? Because the latter took a long time for each run...

I'll really appreciate it if you could give me a hint!

Hongpu

joellembatchou commented 4 months ago

Hi Hongpu,

Step 1 is run across the genome so you should use a genotype file that combines variants genome-wide (hence the hint in the UKBB tutorial to merge the genotype files across chromosomes for step 1).

Cheers, Joelle