Hi , I have data that has 3 column SNPs their gene based on Annovar and a pvalue for every SNP . What I would like is to aggregate the p values for every gene . I know that their is a dependence between the pvalues and I don't know the dependence structure. so fisher method won't work . I read about some methods here : https://arxiv.org/pdf/1212.4966.pdf . And came upon this :

6.1 A rule of thumb First we state a crude rule of thumb for choosing r. Since any method based on the observed values of p1, . . . , pK would affect the validity of the method (see Subsection 6.3), we have to rely on prior or side information for a suitable choice of r. As a rule of thumb, if there is potentially substantial dependence among the p-values, then we should not use Bonferroni, and the harmonic mean might be a safer choice. If we are certain that the dependence is really strong, then the geometric and the arithmetic means might be an even better option. See Subsection 6.4 for a simulation study illustrating this poin.

Based on the article would be happy if you could share your knowledge in this situation what technic is best to use for pvalue aggregation.