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.

severus v0.1.0

The initial release of Severus