HaploPainter

HaploPainter visualizes haplotype information within pedigrees to aid gene mapping in Mendelian diseases.

Key Features:

• Pedigree Visualization: Annotates pedigrees with detailed haplotype data to display inheritance patterns and relationships within families.
• Haplotype Compression: Compresses large haplotypes to represent high-density marker panels that include thousands of single nucleotide polymorphisms (SNPs).
• Marker Section Cut-Out: Cuts out and highlights specific marker sections within haplotypes to focus analysis on regions of interest.
• Compatibility with Linkage Programs: Imports haplotypes calculated by common linkage analysis programs for integration with linkage workflows.

Scientific Applications:

• Gene Mapping in Mendelian Diseases: Supports identification of the smallest critical intervals containing gene defects through pedigree-based haplotype analysis.
• Genome-Scan Data Interpretation: Facilitates interpretation of large datasets generated by genome scans using high-density SNP panels.

Methodology:

Performs haplotype compression and marker-section cut-outs and imports haplotypes produced by common linkage analysis programs; implemented in Perl.