The notebook scripts are ordered based on the presented results in our main paper.
    TAD_boundary_calling.ipynb: The codes for generating the insulation score file and TAD boundary file along with the TAD boundary score for each sample and the merged call set.
    Comprehensive_TAD_catalog_integration.ipynb: The codes for generating the Integrative TAD Catalog.
    Identification_of_TAD-SV.ipynb: The codes for identifying the TAD-SV set.
    Homo_Heter_effect_TAD-SV.ipynb: The codes for analyzing the homozygous SVs and heterozygous SVs' impact on the 3D genome.
    Identification_of_TAD-SV-QTL.ipynb: The codes for identifying the TAD-SV-QTL set.
    Causal_mediation_analysis.ipynb: The codes for performing the causal mediation analysis among SV, TAD structure, and QTL.
    Replication_of_TAD-SV.ipynb: The codes for replication of the TAD-SV set in another independent dataset.
    permutation.sh: The bash script for permutation test to examine the enrichment/depletion between the interested regions in our study.

