RecView

RecView: Recombination Detection and Visualization Using Three-Generation Pedigree Genotype Data

RecView identifies and visualizes recombination events in whole-genome genotype datasets by analyzing grandparent-of-origin of informative alleles across offspring within three-generation pedigrees.

Key Features:

• Recombination Inference Algorithms: Implements two algorithms: one detects shifts in the proportion of alleles with a specific grandparent-of-origin, and another evaluates continuity of alleles sharing the same grandparent-of-origin to infer recombination positions.
• Whole-Genome Genotype Analysis: Processes genotype data across chromosomes or scaffolds and multiple offspring to localize recombination events genome-wide.
• Base-Pair Resolution Reporting: Reports putative recombination positions in base pairs with an estimated precision metric derived from local density of informative alleles.
• Pedigree-Based Allele Tracking: Analyzes grandparent-of-origin for all informative alleles along each chromosome to characterize genetic reshuffling across generations.

Scientific Applications:

• Evolutionary and Population Genetics: Quantifies recombination along chromosomes to investigate genetic evolution, selection, drift, and genomic dynamics; demonstrated using genotype data from the great reed warbler (Acrocephalus arundinaceus).

Methodology:

RecView infers recombination positions by tracking grandparent-of-origin patterns of informative alleles across offspring in three-generation pedigrees, detecting proportion shifts and continuity breaks along chromosomes or scaffolds, and estimating positional precision based on local informative allele density.