pepa

pepa visualizes and quantifies genomic inheritance by processing VCF files, assigning ancestries to homozygous SNPs, and generating comparison tables and chromosome paintings to analyze inheritance patterns.

Key Features:

• VCF Processing: Processes VCF files as input for inheritance analysis.
• Ancestry Assignment: Assigns ancestries to homozygous SNPs.
• Region Clustering: Clusters SNPs into biologically meaningful regions.
• Quantitative Analysis: Generates human-readable comparison tables showing parental contributions at nucleotide and gene levels.
• Chromosome Painting: Visualizes inheritance patterns with chromosome paintings through R.
• Modular Design: Modular architecture with minimal dependencies allows adaptation to diverse organisms.

Scientific Applications:

• Recombination Pattern Analysis: Reveals non-uniform recombination patterns, including chromosomes largely inherited from one parent and seemingly random recombination events.
• Parental Contribution Quantification: Quantifies differences in parental contributions to offspring genomes at nucleotide and gene levels.
• Inheritance Pattern Comparison: Compares genomic regions inherited between offspring, showing that similar parental percentages do not mean identical inherited regions.
• Cross-Organism Inheritance Studies: Adapts to diverse organisms for studying genomic inheritance and recombination dynamics.

Methodology:

pepa processes VCF files, assigns ancestries to homozygous SNPs, clusters them into biologically meaningful regions, and generates comparison tables and chromosome paintings through R.