a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02866-4">aging</a>, and <a href="https://journals.sagepub.com/doi/full/10.1177/1176935119828776">cancer</a>.
Unlike the <code>pileup</code> method in <code>modkit</code> which aggregates the modification calls per genomic position, <code>modkit entropy</code> looks at the co-occurrence of methylation status on individual reads and so the input is a modBAM not a pileup.
To quote <a href="https://doi.org/10.1371/journal.pcbi.1010946">