How do I merge imputed GWAS data

How do I merge imputed GWAS data


I have a cohort that part of the participants were genotyped using the Illumina 2.5M DNA microarray chip and another group of participants using H3Africa chip. I have imputed them using HRC server. To increase the power for my association analyses, I would like to merge them before I conduct the GWAS rather than doing a meta-analysis after the GWAS. I have read that I should only merge intersecting (common in both datasets) SNP. I know how to do this for unimputed data using PLINK2, but I don’t know how to do this in imputed data with several chromosomes. Does some have any lead on this? Any help would be greatly appreciated.




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