Wham

Wham detects structural variants from short read sequencing datasets and performs association testing to link SVs to phenotypes and enable interpretation of genetic variation.

Key Features:

• Integrated Framework: Combines structural variant calling with association testing in a single analytical framework.
• Optimization for short read data: Addresses challenges in identifying SVs from short read sequencing datasets to improve detection accuracy for downstream analyses such as disease-gene identification.
• Benchmarking Performance: Has been rigorously benchmarked against Lumpy, Delly, and SoftSearch, demonstrating superior performance in identifying structural variants.
• Phenotype Association: Associates identified structural variants with phenotypes across species, with examples including humans, domestic pigeons, and vaccinia virus.

Scientific Applications:

• Disease-gene discovery: Enables discovery and association of structural variants with disease phenotypes through integrated calling and testing.
• Comparative and evolutionary genomics: Facilitates analysis of genetic variation and evolutionary changes across species such as humans and domestic pigeons.
• Viral genomics: Supports identification and phenotypic association of structural variants in viral genomes, exemplified by vaccinia virus studies.

Methodology:

Performs structural variant calling from short read sequencing datasets and conducts association testing, with benchmarking performed against Lumpy, Delly, and SoftSearch.