Do you remove blacklisted regions before or after calling peaks?

Question

[cthangav]

Hello, I have a question about ATAC-seq processing. I'm working with mouse data where blacklisted regions typically get removed during processing. Some tutorials remove blacklisted regions from the BAM file before calling peaks. Others do this step afterwards on a BED or NARROWPEAK file. Does the order matter, and if so, which order do you use?