VARista

VARista performs whole-genome variant analysis and prioritization to support interpretation of Variant Call Format (VCF) files and identification of potential disease‑causing variants across hg19, hg38, and T2T reference genomes.

Key Features:

• Whole-genome variant analysis: Processes whole-genome variant data for analysis and prioritization.
• VCF and reference genome support: Accepts Variant Call Format (VCF) files and supports hg19, hg38, and T2T reference genomes with remapping between assemblies.
• Predictive tool integration: Integrates SpliceAI and AlphaMissense for splicing and missense effect prediction.
• Expression data integration: Incorporates tissue- and cell-specific gene expression data for adult and fetal samples to provide biological context for variants.
• Automated PCR primer design: Produces automated PCR primer designs for experimental validation of identified variants.
• Gene summaries and links: Provides gene summaries and external links for genes of interest to support variant interpretation.

Scientific Applications:

• Variant prioritization: Narrowing and prioritizing candidate disease-causing variants for downstream analysis.
• Rare monogenic disease research: Identification and evaluation of putative causal variants in studies of rare monogenic diseases.
• Contextual variant interpretation: Assessment of variant relevance using tissue- and cell-specific adult and fetal expression data.
• Functional impact assessment: Evaluation of splicing and missense effects using integrated SpliceAI and AlphaMissense predictions.
• Experimental validation planning: Design of PCR assays for validation of prioritized variants.

Methodology:

Accepts VCF input, remaps variants between hg19, hg38 and T2T assemblies, integrates SpliceAI and AlphaMissense scores, incorporates tissue- and cell-specific adult and fetal expression datasets, and performs automated PCR primer design.