Severus v1.7

Bug Fixes

• Fixed issues related to VCF format handling.

• Resolved problems in Panel of Normals (PoN) filtering.

New Features

• Added a new parameter for diploid genotyping:

--use_germline_genotype – enables the use of germline genotyping.

Severus v1.6

Fixes

1. Improved handling of overlapping alignments.
2. Better support for SVs with low read coverage.
3. Resolved bugs reported in #57, #51, and #55.

New Feature

• Added support for a whitelist BED file to include all FAIL SVs that fall within the provided BED regions.

Thanks to everyone for the bug reports, suggestions, and feedback!

Severus v1.5

Minor release to celebrate the paper.
New parameters added --control-cov-thr to control the minimum coverage required in the normal sample for the genotyping.
Minor fix in SV detection with a lower number of support.

Severus v1.4

Minor release to fix plotly plots and size of the deletions.

Severus v1.3

Severus v1.3

1. Improved INS detection and sBND detection.
2. A new extended PON file is provided in the pon folder.
3. New –low-quality parameter for improved SV detection in datasets with inconsistent quality and read length.
4. Genotyping changed to 0/1 for somatic SVs.
5. Update in the VCF format to address the bug reports.

Severus v1.2

With version 1.2:

• Severus now supports PoN input for tumor-only runs. We provide PoN data for GRCh38 and chm13

• Improvements in the failed SV filtering

• Improved single BND detection

• New parameter added: --max-unmapped-seq to define the maximum unmapped sequence between two mapped sequences (length of sequence reported in INSSEQ in the vcf)

• Updates in vcf format:

1. INV and DEL are now restricted to the reciprocal inversions and true deletions with decreased coverage. The rest are represented as BNDs. For reciprocal inversions, instead of representing it with two rows (4 BPs), we will represent it with a single row (2 BPs).

2. Minor fixes in vcf formating.

Severus v1.1

Improvements in

• memory usage and run-time #17

• detection of mosaic SVs in VNTR regions

• single breakend detection: new ALIGNED_POS field added to INFO column to provide the imprecise pair position for the single breakends

Bugs fixed:

• Multiple bam files with the same name #20

• Severus version in vcf outputs #22

• DUP in vntrs #19

• --write_alignments only outputs split reads

We are sincerely grateful to Sergey Aganezov (@aganezov) for testing and feedback.

Severus v1.0

• Update on the complex SV clustering
• New graph format with plotly
• Plotly is now required to run Severus
• A new parameter is added, --use-supplementary-tag, to be used with phasing tools for independent phase supplementary alignments, i.e., HiPhase, LongPhase
• VNTR annotation for indels is added
• --between-junction-ins is added to output unmapped inserts between breakpoints.

Severus 0.1.2

• Update on the complex SV clustering
• Improvements in SV filtering
• New parameter added: --output-read-ids
• Multisample SV option added

Severus 0.1.1

Minor changes in the installation methods, no functional changes.