HiCHap

HiCHap analyzes diploid Hi-C data with phased haplotypes to construct maternal and paternal contact maps and enable allele-specific assessment of chromatin three-dimensional organization.

Key Features:

• Bias Correction: Identifies and corrects allele-assignment biases caused by variable genetic variant density across the genome to improve accuracy of allele-specific Hi-C contact maps.
• Comprehensive Analysis Capabilities: Performs read mapping, constructs maternal and paternal Hi-C contact maps, and identifies compartments, topological domains, and chromatin loops genome-wide.
• Allele-Specific Testing: Provides quantitative analyses of allele-specific chromatin 3D organization to assess the influence of genetic variants on chromatin architecture.
• Haploid Data Support: Supports analysis of haploid Hi-C maps without differentiating homologous chromosomes when phasing is not applied.

Scientific Applications:

• Diploid 3D Chromatin Organization: Enables whole-genome identification and comparison of chromatin compartments, topological domains, and chromatin loops in diploid cells using phased haplotypes.
• Allele-Specific Variant Impact Studies: Facilitates investigation of how genetic variant density and specific variants affect allele-specific chromatin structure and function.

Methodology:

Implements a novel bias-correction strategy for allele-assignment biases due to variable genetic variant density and integrates read mapping, construction of maternal and paternal Hi-C contact maps, genome-wide identification of compartments, topological domains, and chromatin loops, and quantitative allele-specific testing.