hzAnalyzer

HzAnalyzer detects, quantifies, and visualizes contiguous homozygosity (runs of homozygous loci) in high-density single nucleotide polymorphism (SNP) datasets to support analysis of homozygous segments in genetic, population history, and selection studies.

Key Features:

• Detection of Homozygous Segments: Identifies contiguous regions of homozygosity (runs of homozygous loci) within high-density single nucleotide polymorphism (SNP) datasets.
• Quantification of Local Genomic Structure: Quantifies local genomic structure by measuring the distribution and frequency of homozygous segments across samples or populations.
• Identification of Outstanding Regions: Highlights genomic regions that exhibit significant or outstanding patterns of homozygosity for downstream analysis.
• Visualization Capabilities: Produces comparative visualizations of homozygous segments across population samples.
• R package implementation: Implemented as an R package for analysis of high-density SNP genotyping datasets.

Scientific Applications:

• Monogenic Disorder Research: Aids identification of causal variants for monogenic disorders by locating runs of homozygosity that may harbor recessive disease alleles.
• Population History Studies: Enables comparison of homozygous segment patterns across populations to infer historical demography and migrations.
• Natural Selection Analysis: Detects regions under selection by identifying excess homozygosity indicative of selective sweeps or local adaptation.

Methodology:

Extracts and quantifies contiguous homozygosity from high-density single nucleotide polymorphism (SNP) datasets using algorithms, applies statistical methods to assess local genomic structure of identified segments, and generates visualizations of homozygous regions.