wgs-structvar

wgs-structvar standardizes calling and filtering of structural variants from whole-genome sequencing to enable population-aware detection and interpretation using SweGen frequency data.

Key Features:

• Standardized Variant Calling: Provides a systematic approach to identifying structural variants from whole-genome sequencing data to ensure consistency in variant detection.
• Comprehensive Filtering Mechanism: Applies filtering that leverages population frequency data to distinguish common and rare structural variants.
• Integration with SweGen Data Set: Uses SweGen population frequencies, including over 29.2 million SNVs and 3.8 million indels from a cohort of 1,000 Swedish individuals, for frequency-based annotation and filtering.
• Detection of Novel Variants: Identifies variants absent from existing databases, with samples contributing on average 7,199 individual-specific variants and 8,645 larger structural variants per individual.
• Population-Specific Insights: Reflects the genetic structure of the Swedish population to support population-aware variant interpretation.

Scientific Applications:

• Clinical Genetics: Identification and characterization of structural variants relevant to genetic disorders for diagnostic interpretation.
• Genetic Epidemiology: Support for association studies through a detailed map of structural variants within a well-characterized population cohort.
• Population Genetics: Analysis of population structure and genetic diversity using population-specific SV frequency data.

Methodology:

Analysis of high-density SNP-array data from >10,000 individuals, selection and whole-genome sequencing of representative samples, and automated pipelines for alignment, variant calling, and quality control.