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However, you need to be cautious that any artefacts between cases and control will be estimated as 'genetic' variance, especially when cases and controls were genotyped separately (e. on different plate or at different labs). When using GCTA to analysis a case-control study, very stringent QC on SNPs are required. Please refer to Lee et al (2011 AJHG) for the QC steps and some other technical details of applying the method in case-control studies.
It may also suggest that the true parameter (i.