HiFiCNV v1.0.1

v1.0.1 - 2024-10-21

Fixed

• Improve minor allele frequency VCF parsing (#31)
  • Allow for and filter out unknown AD values
  • Improve error message to include VCF lines that can't be parsed

HiFiCNV v1.0.0

v1.0.0 - 2024-03-27

This release includes minor ease-of-use improvements, CNV output should be unchanged. The release version is updated to 1.0 to reflect that HiFiCNV is now operating as a stable part of our HiFi WGS pipeline.

Added

• Add progress reporter to alignment scan

Changed

• Accelerate depth bin GC content computation
  • Improve and parallelize algorithm to reduce fixed runtime overhead by ~5 min for human genome analysis with typical thread counts.

Fixed

• Improve error message for failed depth estimation (#25)
• Improve error message for unmapped BAM input (#24)
• Improve error message for mismatched reference and BAM chromosomes (#23)
• Improve error message when BAM index is missing (#22)

HiFiCNV v0.1.7

v0.1.7 - 2023-08-22

Added

• Add new data files to partially support hg19 and hs37d5

Changed

• Rename expected copy number example files from male/female to XY/XX

Fixed

• New FAQ section to explain common errors
• Improved error message for cov-regex mismatch
• Improved error messaging for mismatches between aligned BAM contigs and provided reference file contigs

HiFiCNV v0.1.6b

Fixes

• Corrects an error in the uploaded binary build.

HiFiCNV v0.1.6

v0.1.6 - 2023-03-29

Additions

• Added support for minimap2-aligned BAM files, fixes #4 and fixes #6
• Updated quickstart to specify supported upstream tools

Fixed

• Improved error messaging for cov-regex mismatch

HiFiCNV v0.1.5

v0.1.5 - 2023-03-14

Fixed

• Adjust linux release build process to improve portability
  • If you've experienced immediate segfaults trying to run the previously released HiFiCNV binary on your linux distribution (especially older ones), update to this version.
  • This release should be functionally identical to v0.1.4 so no update is needed for users without binary issues.

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hificnv-v0.1.5-x86_64-unknown-linux-gnu.tar.gz is a tarball containing the binary distribution for 64-bit linux.

HiFiCNV v0.1.4

v0.1.4 - 2023-03-13

Fixed

• Fixes a bug where optional files were being treated as required (HIFICNV-2)

HiFiCNV initial release

Initial release for HiFiCNV:

• Ingests a HiFi aligned BAM file for read depth
• Calculates copy number estimates using read depth
• Outputs copy number changes relative to expected values into a VCF file
• Additionally provides auxiliary data tracks for visualization