github.com/iwc-workflows/consensus-peaks/consensus-peaks-atac-cutandrun

Identifies high-confidence consensus peaks from ATAC-seq or CUT and RUN replicate experiments. The workflow calls peaks on individual replicates and identifies their intersection. To control for sequencing depth differences, it subsamples all replicates to the smallest library size, performs peak calling on the combined normalized data, and retains only peaks whose summits overlap with intersections from a user-defined minimum number of replicates.