OnTAD repo: https://github.com/anlin00007/OnTAD
Create Imput with: create_dense_matrix.py
Use there docker: singularity run docker://anlin00007/ontad:v1.2
Run there tool with following parameters:
OnTAD tmpdata/G2.fc_1_2.wOldG2.chr18.cis.matrix -penalty 0.1 -maxsz 200 -bedout 18 78077248 50000 -o OnTAD_cis_chr18