variance of variant effects within a gene, and whether that variance is larger than expected by chance. That is, do the variant effects differ from zero more than expected by chance? In SKAT we tested both MAF = 0.01 and MAF = 0.05. The purpose of using both VT and SKAT is that they each achieve greater statistical power in complementary scenarios. VT is most powerful when all minor alleles within a gene have the same direction of effect and has low power when minor alleles have opposite directions of effect. SKAT has the same power regardless of whether the minor alleles within a gene have opposite or the same directions of effect.
