sage v3.4.2

Technical:

• allow adjacent indel to SNV in NovaseqX artefact logic

orange v3.3.0

Changes:

• Clonal likelihood is set to 0 or 1 based on variant copy number when converting germline variants to somatic
• Bugfix: Fix bug in germline MVLH parsing that caused them to be underestimated by a factor 100.
• Restrict germline MVLH table on PDF and related field in JSON to genes handled by SAGE germline.

mark-dups v1.1.2

Bugs:

• only unmap supplementaries if their primary satisfies standard primary-mate criteria

purple v4.0.2

Functional:

• exclude SVs from VCF if on chrY and gender is female

sage v3.4.1

Functional:

• addresses issues from NovaseqX artefacts: use base qual from 8+ homopolymer upstream of variant

mark-dups 1.1.1

Technical:

• handle input BAMs with the same read group ID as happens when fastqs are split for alignment

teal v1.2.2

Bug fix:

• Fix crash when processing none standard chromosome names
• Fix crash when processing unpaired reads

bam-tools v1.2.1

Bugs:

• fixed crash when running with a single thread

Technical:

• BamSlicer - slice all contigs, order by expected load, handle multiple reads in remote region

orange v3.2.0

• Support new ORANGE-datamodel (v2.3.0).
• Support germline deletions heterozygous in the tumor:
  • Included in new section "Potentially pathogenic germline LOH events" on PDF report.
  • Included in new fields allGermlineLossOfHeterozygosities and reportableGermlineLossOfHeterozygosities in the JSON.
  • Converted to somatic LOH events when convert_germline_to_somatic parameter is provided.
  • Changed titles of somatic LOH and germline losses on PDF report to accommodate these changes.
• Combine multiple germline loss calls for the same gene into one call.
• Merge germline and somatic losses when both exist for the same gene.
• ORANGE throws an exception in case empty cuppa predictions are provided (cuppa output file is empty or is missing probabilities)

Bugfix:

• Simple clusters affecting no exons are now excluded when counting expected number of linx plots
• ORANGE throws an exception in case a cancer type is resolved for isofox that does not exist in the gene distribution data.

sigs v1.2.1

Bugs:

• fixed reporting of tool version