GAMIBHEAR

GAMIBHEAR reconstructs whole-genome haplotypes from Genome Architecture Mapping (GAM) data to enable allele-specific analysis of chromatin contacts.

Key Features:

• Allele-specific phasing: Enables haplotype reconstruction and phasing directly from GAM data by leveraging allelic observations.
• GAM-specific probabilistic model: Implements a GAM-specific probabilistic model that aggregates allelic co-observation frequencies to optimize phasing accuracy.
• Benchmarking and validation: Validated using a hybrid mouse embryonic stem cell line with known haplotype structure to assess correctness and completeness.

Scientific Applications:

• Allele-specific chromatin contact analysis: Enables allele-specific analysis of chromatin contact points captured by GAM.
• Genome-wide haplotype inference from low-input data: Infers genome-wide haplotypes from low-input GAM datasets, enabling analyses on limited material.
• Non-model organisms and unknown haplotypes: Supports haplotype reconstruction in non-model organisms or individuals with unknown haplotypes to broaden genetic and epigenetic studies.

Methodology:

Aggregating allelic co-observation frequencies from GAM datasets; applying a GAM-specific probabilistic phasing model tailored to GAM characteristics; and validating reconstructed haplotypes using benchmark datasets, including a hybrid mouse embryonic stem cell line with known haplotype structure.