Copy number variant caller and visualization utilities for HiFi sequencing data
HiFiCNV is a copy number variant (CNV) caller optimized for HiFi reads. Key features include:
- Segmentation and calling optimized for HiFi germline WGS
- Automatic GC-bias estimation and correction
- Generates bigwig tracks for depth and allele frequency to visualize CNV-scale events in IGV
- CNV output in bedgraph and VCF formats
- Efficient multi-threaded analysis
Authors: Chris Saunders, Matt Holt
Please note that HiFiCNV is still in early development. We are still tweaking the input / output file formats and making changes that can affect the behavior of the program.
- Installation instructions
- Quickstart example
- Output files
- Methods
- Performance
- Auxiliary file generation
If you notice any missing features, bugs, or need assistance with analyzing the output of HiFiCNV, please open a GitHub issue.
HiFiCNV 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 HiFiCNV lives up to the quality that PacBio strives for, we make no warranty regarding this software.
As HiFiCNV 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 HiFiCNV 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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