inGAP-sv

inGAP-sv detects and visualizes structural variations from paired-end mapping data to characterize large and complex structural variants for genomic and genotype-phenotype analyses.

Key Features:

• Detection of Structural Variants: Identifies structural variations by clustering abnormally mapped read pairs based on gap signatures and detects a wide range of SVs including large insertions and complex variants.
• Visualization of Structural Variants: Produces visual representations of structural variations derived from paired-end mapping data.
• Quality Evaluation: Evaluates predicted structural variants using local depth of coverage, mapping quality, and associated tandem repeats.
• Reduced False Discovery Rate: Achieves a lower false discovery rate compared to existing methods.

Scientific Applications:

• Personal-genome variation mining: Mines genetic variation from personal genomes to support analyses of individual genomic differences.
• Genotype–phenotype studies: Supports investigations into genotype-phenotype relationships by detecting complex structural variants.
• Personalized medicine: Facilitates identification of clinically relevant structural variants for personalized medicine research.
• Evolutionary biology and genomic research: Enables detection and analysis of large and complex SVs for evolutionary and broader genomic studies.

Methodology:

Processes paired-end mapping data by clustering abnormally mapped read pairs based on gap signatures to detect structural variants and evaluates predicted variants using local depth of coverage, mapping quality, and associated tandem repeats.