OctopusV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and...

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Structural variants (SVs) are crucial for genomic variability and disease.
• Accurate SV analysis across diverse samples and sequencing platforms is a significant challenge.

Purpose of the Study:

• To develop a computational tool, OctopusV, for standardizing structural variant annotations.
• To enable robust cohort-specific variant identification through flexible integration of variant calls.
• To provide an end-to-end solution for structural variant analysis from raw data to final callsets.

Main Methods:

• OctopusV standardizes ambiguous breakend (BND) annotations into canonical SV types (inversions, duplications, translocations).
• It integrates variant calls using set operations (union, intersection, difference, complement).
• TentacleSV provides an automated pipeline for an end-to-end workflow.

Main Results:

• OctopusV demonstrates improved precision, recall, and consistency in SV analysis.
• The integrated approach facilitates cohort-specific variant identification.
• The tools offer a comprehensive solution for structural variant detection.

Conclusions:

• OctopusV and TentacleSV provide a valuable end-to-end solution for structural variant analysis.
• These tools enhance accuracy and consistency, aiding cancer genomics and rare disease diagnostics.
• The standardized approach improves the reliability of variant callsets across studies.