Use REGENIE for Baseline GWAS Analysis

[Rafaeladoliveira]

I’m looking to confirm if REGENIE can be used for a genotyped-only GWAS (no imputed data).

Is the following workflow valid?

Step 1: Use a subset of LD-pruned genotyped SNPs.

Step 2: Use the full set of non-pruned genotyped SNPs.

Or is Step 2 strictly intended for WGS/imputed data? Do you think is better use PLINK for association testing on genotyped-only data?

[joellembatchou]

Hi,

Yes in step 2 you have flexibility as to what variants to analyze (array, imputed, exome...)

Cheers,
Joelle