RareVariantVis

RareVariantVis visualizes and annotates rare genomic variants from whole genome sequencing (WGS) data to support identification and interpretation of coding and non-coding variants relevant to monogenic rare diseases.

Key Features:

• Comprehensive visualization: Visual representation of variants along chromosomes including chromosomal position, zygosity, and allele frequency.
• Variant flagging: Distinct flagging of rare variants and de novo variants for genome-wide and per-chromosome inspection.
• Annotation: Annotation of variants with dbSNP identifiers, gene associations, and recorded inheritance patterns.
• Support for variant types: Analysis of both germ line and somatic variants from WGS data.
• Coding and non-coding region analysis: Inclusion of variants from coding and non-coding regions to aid detection of disease-relevant non-coding variation.
• Scalability and organization: Designed to handle large WGS datasets with global and per-chromosome organization of variant data.

Scientific Applications:

• Rare disease genetics: Identification and prioritization of candidate causative variants in monogenic rare disease studies using WGS.
• De novo variant discovery: Detection and characterization of de novo variants relevant to inherited and sporadic genetic disorders.
• Cancer genomics: Analysis of somatic variant landscapes alongside germ line variation in cancer studies.
• Non-coding variant interpretation: Exploration of non-coding regions from WGS to identify potential regulatory or pathogenic variants.

Methodology:

Annotating, filtering, and presenting genomic variants with data organized globally and per chromosome; performance demonstrated using the Genome in a Bottle WGS dataset.