SVTopo represents complex structural variants (SVs) to enhance PacBio HiFi data. SVTopo determines connections between SV breakends using aligned reads and, optionally, variant calling output from the sawfish variant caller. SVTopo outputs connected breakends as JSON data and uses the SVTopoVz python utility to plot complex structural rearrangements as high-quality images.
Key Features (see Result Interpretation for more details):
- Top section: illustration of connected aligned sequences as blocks, showing order and orientation in the sample genome relative to the reference
- Alignment support strength shown by block weight
- Block sizes encoded into legend
- Optional gene annotations
- Bottom section: chained plot highlighting deletion, duplication, and inversion effects on rearranged genome structure
Example SVTopo image from HG002 rearrangement
- See the Getting started section in the User Guide to start using SVTopo
- See also Result interpretation for examples and explanation of SVTopo images
SVTopo is a pre-release software intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that SVTopo lives up to the quality that PacBio strives for, we make no warranty regarding this software.
As SVTopo is not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists or PacBio Customer Service for assistance with any HiPhase release. Please report all issues through GitHub instead. We make no warranty that any such issue will be addressed, to any extent or within any time frame.
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