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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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Meaning of --bsize option in step 2 #239

Closed bicyclic closed 2 years ago

bicyclic commented 2 years ago

Hi Joelle,

What's the interpretation of the --bsize option in step 2? Is it supposed to be set to the same value that was used in step 1? Just reviewed the paper again, and I am only able to appreciate block size discussed in reference to step 1 where array SNPs are partitioned into blocks of bsize SNPs for block-by-block ridge regression.

Thanks!

joellembatchou commented 2 years ago

Hi,

Step 2 just analyzes variants in parallel so the value of block size has no effect on the summary stats output. It is mainly dependent on how much memory you have available on the machine (we used block size of 400 in the Regenie paper).