Releases: hartwigmedical/hmftools
Releases · hartwigmedical/hmftools
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
purple v4.0.1
Bugs:
- Block
LOW_TUMOR_VCN
filtered variants from being reportable
purple v3.9.4
Bugs:
- Block
LOW_TUMOR_VCN
filtered variants from being reportable
sigs v1.2
Technical:
- added version info
- compatibility with Purple v4.0 (new germline status types)