So what is the best practice for GWAS RNA-seq quantification? GWAS does not compare different gene expression in each sample. However, it's very important that expression of the same gene is normalized well across sample.

I know RPKM is probably the best choice. So is RSEM better or TPM better. If using RSEM and TPM, do we need to do further normalization? (I know TCGA set up quantile of RSEM to 1000 in order to roughly normalize across samples)