Hi @Yann Vanrobaeys we were thinking about how to best implement this. The way you propose with performing DMR between different tumour samples seems more like a step downstream of the pipeline to us. We want to have peolpe be able to run dozens of samples at a time and the combinatorial DMRs for all samples would be a lot of compute and output. What we would like to implement is to perform these steps between haplotypes and, if present, tumour/normal pair. Unless you have a way on how to do it between samples in a clean way.