Overlap CNV with ENCODE DNAse-seq peaks

Question

[QVINTVS_FABIVS_MAXIMVS]

I have a list of CNVs in BED format and I would like to annotate as likely disrupting accessible DNA regions.

I assume that a naive intersection is not good enough. What are some approaches in annotating genomic positions to DNAse-seq peaks from ENCODE?

Or should I be working with different data, like the BAM files?

Answer 1

[Sinji]

You could possibly use bedtools closest to annotate CNV positions to the nearest DNAse-seq peak.