Svx is a merging tool for structural variations (SVs) and copy number variations (CNVs) called by sawfish from PacBio HiFi sequencing data. Svx is largely inspired by Jasmine, which frames multi-sample SV merging as a graph problem and uses a modified minimum-spanning-forest strategy to merge analogous variants across samples. Svx follows the same high-level philosophy while implementing its own Rust-native merge engine and constraints. Beyond the core merge algorithm, svx includes many ergonomic features, a few examples: built-in parallelization across (and within) contigs, TR support, global sorting on output, easy run scoping by contig and region, and selection of SV classes to include in the merge.
This is an early release of svx and is under development. Expect breaking changes at all levels, data formats, and system behavior.
- Currently only the sawfish SV/CNV calling tool is supported.
Current version: 0.6.0.
For a complete changelog, see the changelog or the git history.
- The latest svx Linux binary is available here
- Documentation index
- Usage guide
- Tuning and defaults
- Output interpretation
- TR containment
- Merge constraints
- Command line interface (generated reference)
If you notice any missing features, bugs, or need assistance with analyzing the output of svx, please do not hesitate to reach out by email or open a GitHub issue.
Svx is currently in active development and is intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that svx lives up to the quality that PacBio strives for, we make no warranty regarding this software.
As svx 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 svx 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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