sawfish - sawfish v2.0.5

v2.0.5 - 2025-08-27

Changed

• CR-531 Improve verification of expected copy number file [PacificBiosciences/sawfish#26]

Fixed

• CR-539 Consistently convert all non-ACGT bases from both reference and read sequences to N [PacificBiosciences/sawfish#27]

- Rust
Published by ctsa 6 months ago

sawfish - sawfish v2.0.4

v2.0.4 - 2025-08-14

Added

• CR-523 Allow joint-call input sample data to be specified as a CSV file
  • This update allows all input sample paths to be specified in one file provided with the --sample-csv argument
  • The sample CSV file also allows alignment file paths to be specified for each sample, to avoid reusing the file paths specified during the discover step.
  • Also added ability to optionally specify a new reference file path for joint-call
  • All previous joint-call sample input command-line formatting is still valid

- Rust
Published by ctsa 6 months ago

sawfish - sawfish v2.0.3

v2.0.3 - 2025-07-24

Changed

• CR-513 Add disable-cnv option to the discover step
  • Disables GC-bias estimation, depth segmentation and CNV calling for the given sample
  • May be helpful for certain non-WGS sample inputs

Fixed

• CR-516 Fix panic which could infrequently occur during multi-sample copy number boundary sync

- Rust
Published by ctsa 7 months ago

sawfish - sawfish v2.0.2

v2.0.2 - 2025-07-11

Added

• Add support for cram file inputs which include bzip2 and lzma codec blocks [PacificBiosciences/sawfish#19]

- Rust
Published by ctsa 8 months ago

sawfish - sawfish v2.0.1

v2.0.1 - 2026-06-18

Added

• CR-497 Add GC-bias corrected depth track to the per-sample output from joint-call

- Rust
Published by ctsa 8 months ago

sawfish - sawfish v2.0.0

v2.0.0 - 2025-05-19

This is the first official release of SV/CNV integration in sawfish. This version adds full depth segmentation into the SV calling process to provide several benefits:

1. Consistent view of all large variants in a single output, including calls based on breakpoint evidence, calls from depth evidence and calls jointly supported by both.

2. A breakpoint-enhanced CNV caller: Sawfish provides standard depth-based CNV calls without requiring breakpoint evidence, but when available, breakpoints can be used to provide more accurate segmentation and higher sensitivity at lower sequencing depths.

3. An improved SV caller, via more precise calling of large, unbalanced SVs: All large deletions and duplications must have some level of depth segmentation support, enabling more precise large variant output.

- Rust
Published by ctsa 9 months ago

sawfish - sawfish v1.0.2

v1.0.2 - 2025-04-25

Changed

• CR-480 Convert large deletions and duplications to breakends
  • Deletions and duplications larger than 100kb are now converted to breakend records by default, can be changed with --max-deldup-size argument in the joint-call step.

Fixed

• CR-470 Improve validation of sample discover step input
  • Provide clear usage error if any input samples to the joint-call step do not appear to be complete sawfish discover step results

- Rust
Published by ctsa 10 months ago

sawfish - sawfish v2.0.0a7

v2.0.0a7 - 2025-04-18

This is the first public alpha release of SV/CNV integration. This version of sawfish adds full depth segmentation into the SV calling process to provide (1) independent depth-based CNV calls, (2) integrated calls with both breakpoint and depth support and (3) to improve filtration of large putative breakpoint-based DEL/DUP calls without depth support.

Status: This is an alpha release. The first full round of single and multi-sample SV and CNV integrations are in place, with a full user guide update. The integrations likely still need polish and further attention on more practical use cases, as well as more complete documentation. The current behaviors, cmdline arguments and file formatting may all be subject to change prior to a stable release of CNV integration.

- Rust
Published by ctsa 10 months ago

sawfish - sawfish v1.0.1

v1.0.1 - 2025-04-13

Fixed

• CR-468 Fix high memory usage when joint-genotyping from CRAM (github #15)
  • This issue only impacts analysis from CRAM, all BAM-input analysis is unaffected.
  • The excess memory usage had only a minor effect on single-sample analysis, but could become very large at higher sample and thread counts.
• CR-469 Fix very low-frequency non-deterministic genotyping result
  • This also fixes non-deterministic read order in the optional supporting reads output

- Rust
Published by ctsa 11 months ago

sawfish - sawfish v1.0.0

v1.0.0 - 2025-04-10

The v1 release marks the initial stabilization of sawfish with its publication in Bioinformatics. This version is functionally identical to v0.12.10 but includes updated in-source documentation for both accuracy assessment and methods.

Added

• CR-467 Add in-source pandoc sawfish methods document.

Changed

• CR-462 Updated accuracy assessment page from the original sawfish release to match all updated methods reported in the Bioinformatics paper.

- Rust
Published by ctsa 11 months ago

sawfish - sawfish v0.12.10

v0.12.10 - 2025-02-24

Fixed

• Fix handling of chromosome names with colons, eg. 'HLA-DRB1*10:01:01' (github #11)

- Rust
Published by ctsa 12 months ago

sawfish - sawfish v0.12.9

v0.12.9 - 2025-01-10

Added

• CR-418 Provide BAM output of assembled SV contig alignments in the joint-call step
  • BAM output reflects all assembled SV haplotypes used during genotyping, which can be useful for reviewing SV calls

- Rust
Published by ctsa about 1 year ago

sawfish - sawfish v0.12.8

v0.12.8 - 2024-12-13

Fixed

• Increase system open file limit (github #9)
  • May simplify joint-call for large pedigrees at high thread counts
• Improve error message when split reads map to an unknown chromosome (github #8)

- Rust
Published by ctsa about 1 year ago

sawfish - sawfish v0.12.7

v0.12.7 - 2024-10-23

Fixed

• Fix "Illegal Instruction" error reported for some use cases (github #3)
  • Removed gcc native cpu optimization in WFA2-lib believed to be causing this issue
  • Added additional --debug output to discover mode contig alignment logic

- Rust
Published by ctsa over 1 year ago

sawfish - sawfish v0.12.6

v0.12.6 - 2024-10-15

Fixed

• Fix discover mode input path canonicalization (reversed flag logic)

- Rust
Published by ctsa over 1 year ago

sawfish - sawfish v0.12.5

v0.12.5 - 2024-10-14

Added

• Add new joint-call --report-supporting-reads option to report read names supporting each variant

Changed

• CR-390 Canonicalize all discover mode input paths
  • Also provide new --disable-path-canonicalization discover step option to store input paths as-is
• CR-391 Don't create output directory until command line is validated

- Rust
Published by ctsa over 1 year ago

sawfish - sawfish v0.12.4

v0.12.4 - 2024-09-13

Added

-CR-384 Add debug logging option - High detail level intended to improve crash reports from external users - Initially populated for breakpoint refinement only, debug log coverage will be expanded as required - Expose clobber option to overwrite existing output directory

Fixed

-CR-385 Improve error message for unexpected alignment patterns from VACmap - This also adjusts some off-by-one errors in neighbor extension handling, which could cause infrequent changes to inversion output - Note VACmap is still unsupported; working towards clear error messages for problematic alignments from any source

- Rust
Published by ctsa over 1 year ago

sawfish - sawfish v0.12.3

v0.12.3 - 2024-09-03

Fixed

-CR-378 Improve error message for hard-clipped split read input -CR-379 Improve error message when discover directory is missing

- Rust
Published by ctsa over 1 year ago

sawfish - sawfish v0.12.2

v0.12.2 - 2024-08-21

Fixed

-CR-377 Remove rq tag requirement in input alignment records

- Rust
Published by ctsa over 1 year ago

sawfish - sawfish v0.12.1

v0.12.1 - 2024-08-08

Fixed

• CR-375 Fix infrequent discover mode failures due to invalid breakpoint ranges.
  • Issue seems to have started with v0.12.0 via CR-340

- Rust
Published by ctsa over 1 year ago

sawfish - sawfish v0.12.0

v0.12.0 - 2024-05-23

Added

• CR-327 Add local SV phasing
  • Short-range phasing provided in VCF records wherever multiple hets are genotyped on one or more overlapping SV haplotypes

Changed

• CR-340 Improve handling of multi-breakpoint haplotypes
  • Improves detection of complex SV breakpoints, especially for small inversions
• CR-333 Adjust alignment for long breakpoint homology
  • Improves detection of high homology inversions
• CR-330 Expand trimmed read search region for small SV regions
  • Improves detection of soft-clipped evidence for low homology insertions

- Rust
Published by ctsa almost 2 years ago

sawfish - sawfish v0.11.0

v0.11.0 - 2024-04-18

Improve a number of discovery and scoring features related to inversions, inverted breakpoints and large deletions.

Changed

• CR-323 Improve scoring for a number of cases relevant to inversions and inverted breakpoints
• CR-321 Change contig flank size handling to improve large inversion calling
• CR-318 Expand trimmed read search region for large SV candidates
  • Improves recall for inverted breakpoints and duplications
• CR-317 Standardize on csi indexing for bam output

Fixed

• CR-324 Fix non-deterministic inversion output

- Rust
Published by ctsa almost 2 years ago

sawfish - sawfish v0.10.0

v0.10.0 - 2024-03-05

Initial github release

- Rust
Published by ctsa almost 2 years ago