HandyCNV

HandyCNV summarizes, annotates, converts, compares, and visualizes copy number variants (CNVs) and runs of homozygosity (ROH) detected from SNP genotyping data to support post-analysis of genomic variation in humans and diploid livestock species.

Key Features:

• Standardization: Provides a consistent framework for processing CNV and ROH data to standardize outputs across projects.
• Comprehensive analysis: Integrates summarization, annotation, conversion, comparison, and visualization of CNVs and ROH in a single analytical suite.
• Reproducibility: Promotes reproducible analyses by applying standardized data-processing procedures for CNV and ROH results.
• Summarization: Aggregates variant calls and generates summary statistics for CNV and ROH datasets.
• Annotation: Links CNVs and ROH to known genomic features to provide biological context.
• Conversion: Transforms data formats for compatibility with other tools and downstream analyses.
• Comparison: Enables comparative analysis of CNV and ROH profiles across samples or populations.
• Visualization: Produces graphical representations of CNVs and ROH to aid interpretation of genomic variation.

Scientific Applications:

• Genomic variation analysis in humans and diploid livestock species: Supports analysis of CNVs and ROH from SNP genotyping data for studies of genetic diversity, disease susceptibility, and evolutionary biology.

Methodology:

Implemented in R, the package accepts SNP genotyping data, handles large-scale genomic datasets, and performs summarization, annotation, conversion, comparison, and visualization of CNVs and ROH.