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CNVs and SVs Interpretation

🔹 Multi SV/CNV Analysis

VarXOmics supports multi-sample CNV (Copy Number Variant) and SV (Structural Variant) analysis.

1. Input Data

  • From the Home page, choose “Multi SV/CNV”.
  • Drop to upload CNV/SV VCF file (e.g., sampleID.cnv.vcf.gz).
  • Click "Run" and the analysis settings will pop-up:
  • Reference Genome (GRCh37 or GRCh38)
  • Variant Type (CNV or SV)
  • HPO ID, separated by comma. (e.g., HP:0031218,HP:0002071)
  • After configuration, click Start Analysis to begin.


2. Results Overview

🧾 Annotated TSV Table

Displays all annotated CNVs/SVs identified across the uploaded samples. CNVs and SVs are annotated by AnnotSV. Users can choose which columns to display via the “Columns” button (top-right corner).

🧬 Circos Visualization

This section presents a genome-wide Circos plot of all identified CNVs and SVs.

3. Export

Users can export all results, figures, and enrichment tables as a single compressed archive by clicking “Export All” in the top-right corner of the interface.