vvv2_display

vvv2_display consolidates variant calling, annotation, and coverage results from viral genome analyses into a PNG visualization and a filtered TSV file to streamline interpretation of significant variants.

Key Features:

• Genome Visualization: Generates a PNG image showing alignment coverage depth and genomic annotations, with significant variants displayed as symbols whose height reflects frequency and shape indicates the affected protein.
• Variant Filtering: Produces a tab-separated (TSV) file listing only high-confidence variants with frequencies, flanking nucleotides, and impacted genes and proteins.
• Cross-Referencing: Assigns each significant variant a unique identifier linking the PNG image directly to the corresponding entry in the TSV file.
• Data Integration: Processes SNP proportions from vardict outputs, CDS annotations from vadr, and coverage depth from samtools depth.

Scientific Applications:

• Viral Variant Interpretation: Enables rapid identification of biologically relevant mutations and deviations from a reference viral genome without manual sifting through dispersed NGS output files.
• Genomic Quality Assessment: Summarizes alignment, variant calling, and annotation analyses for evaluation of viral genome assemblies.

Methodology:

vvv2_display filters and summarizes inputs from vardict (SNP proportions), vadr (CDS annotations), and samtools depth (coverage depth) to generate a PNG image and TSV output.