DESeq2 detects automatically count outliers using Cooks's distance and removes these genes from analysis. It also automatically removes genes whose mean of normalized counts is below a threshold determined by an optimization procedure. Removing these genes with low counts improves the detection power by making the multiple testing adjustment of the p-values less severe.

https://hbctraining.github.io/DGE_workshop/lessons/05_DGE_DESeq2_analysis2.html