HiFiCNV

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

Early release warning

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.

Availability

• Latest release with binary
• Auxiliary data files

Documentation

• Installation instructions
• Quickstart example
• Output files
• Methods
• Performance
• Auxiliary file generation

Need help?

If you notice any missing features, bugs, or need assistance with analyzing the output of HiFiCNV, please open a GitHub issue.

Support information

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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