VCFshiny

VCFshiny performs interactive analysis and visualization of genetic variants in Variant Call Format (VCF) files to support interpretation of next-generation sequencing data.

Key Features:

• Annotation Methods: Supports Annovar and VariantAnnotation to annotate VCF files with gene associations and functional impacts.
• Input Processing: Processes annotated VCF files as inputs for downstream summarization and visualization.
• Variant Summary Statistics: Generates total variant counts and reports overlaps across sample replicates.
• SNP Analysis: Summarizes base alterations in single nucleotide polymorphisms (SNPs).
• Indel Analysis: Reports length distributions of insertions and deletions (indels).
• Mutated Gene Frequency: Identifies high-frequency mutated genes.
• Genomic Distribution: Reports variant distribution across the genome and within specific genomic features.
• Cancer-Specific Analyses: Detects variants present in cancer driver genes and computes cancer mutational signatures.

Scientific Applications:

• Cancer Genomics: Characterizes variants in cancer driver genes and analyzes mutational signatures to inform disease mechanisms and potential therapeutic targets.
• Next-Generation Sequencing Variant Interpretation: Summarizes and annotates VCF-derived variants from next-generation sequencing to aid interpretation of functional impacts.

Methodology:

Implemented in R using the Shiny framework; integrates Annovar and VariantAnnotation and processes annotated VCF files to produce summaries and visualizations.