The UCSC information about the Broad/Encode Histone modification track says:
Discrete intervals of ChIP-seq fragment enrichment were identified using Scripture, a scan statistics approach, under the assumption of uniform background signal.
While Scripture looks like software for RNA-Seq analysis, it seems it can be used for ChIP-Seq analysis using the
-task chip flag. It is not clear that there is a paper that directly describes this use of the software.
Ernst, J., Kheradpour, P., Mikkelsen, T., Shoresh, N., Ward, L., Epstein, C., Zhang, X., Wang, L., Issner, R., Coyne, M., Ku, M., Durham, T., Kellis, M., & Bernstein, B. (2011). Mapping and analysis of chromatin state dynamics in nine human cell types Nature DOI: 10.1038/nature09906