vcfView

vcfView evaluates somatic variant calls from variant call format (VCF) files to assist discrimination of somatic mutations from germline variants, sequencing errors, and other sequencing artifacts.

Key Features:

• Exploration of analytical choices: Examines effects of analytical parameters on mutant allele frequency spectra, mutational signatures, and annotated somatic variants within genes of interest.
• Re-examination of filtered variants: Re-evaluates variants that have been filtered out by variant callers to recover potential true somatic events and inform sensitivity trade-offs.
• Extensibility: Supports integration of additional algorithms that leverage vcfView's VCF preprocessing capabilities for customized analyses.
• R-based data processing: Conducts all data processing using R and includes VCF preprocessing functionality.

Scientific Applications:

• Driver mutation discovery: Supports identification and characterization of novel and low-frequency cancer driver mutations from high-throughput sequencing data.
• Variant quality assurance: Facilitates assessment of sequencing and calling artifacts to improve accuracy of somatic variant calls.
• Analytical optimization: Informs selection of analytical and sample-preparation strategies to enhance mutation detection sensitivity and specificity.

Methodology:

Processes VCF files using R; performs VCF preprocessing; re-evaluates variants filtered by variant callers; computes mutant allele frequency spectra; derives mutational signatures; annotates somatic variants; and permits integration of external algorithms.