reconCNV

reconCNV visualizes copy number variation (CNV) results from high-throughput targeted sequencing (NGS) to summarize genomic gains and losses and allelic imbalance for interpretation.

Key Features:

• Broad caller compatibility: accepts delimited result files from many NGS CNV callers to integrate CNV analysis outputs.
• HTML report output: generates a portable HTML report as a shareable output format.
• CNV track visualization: displays both relative fold change and absolute copy number to represent genomic gains and losses.
• Variant allele fraction (VAF) track: provides a VAF track to visualize allelic imbalance and potential loss of heterozygosity (LOH).
• Artifact masking: supports masking of assay-specific technical artifacts to reduce systematic noise in CNV signal tracks.
• Genome context linking: includes direct links to the UCSC Genome Browser for genomic context follow-up.

Scientific Applications:

• Research and clinical CNV review: applicable in research and clinical review settings for inspection and interpretation of CNVs from targeted NGS data.
• Variant review and reporting: consolidates CNV signal tracks and allelic evidence to support variant review and reporting workflows.
• Hypothesis generation: combines CNV and VAF evidence to aid hypothesis generation about genomic alterations.

Methodology:

Parses delimited result files from NGS CNV callers, displays relative fold change and absolute copy number tracks and a VAF track, applies assay-specific artifact masking, and outputs a portable HTML report with links to the UCSC Genome Browser.