If I just want to use 3 snps from an imputed dataset, where 2 were imputed snps. Would I need to run basic qc procedures again of the merged imputed dataset (snp & sample call rates, hwe, ibd, pca), if the snp passed pre-imputation qc and post imputation info score filter? I know that for gwas types of studies, it is recommended to run post-imputation qc. However, if one is interested in a small subset, say even 1 chromosome, can you just run these sanitary checks on the snps/chr you're testing?
Thank you so much for your input.