isofox v1.0

Initial release with transcription expression, novel splice junctions and fusion calling

See HMF resources page for Isofox resource files:

• Isofox expected count for transcript expression and GC bias
• Ensembl data cache
• known fusions file

bachelor 1.10

1. Optionally include non-PASS variants from a VCF, requires config include_vcf_filtered, marks them as GERMLINE_FILTERED
2. Remove fields DbSnpId and CosmicId
3. Write ClinvarSignificanceInfo to DB
4. Change minorAllele Ploidy to JunctionCopyNumber
5. New 'pathogenic' field - BLACK_LIST, WHITE_LIST, CLINVAR_PATHOGENIC, CLINVAR_LIKELY_PATHOGENIC, CLINVAR_CONFLICTING, CLINVAR_BENIGN, CLINVAR_LIKELY_BENIGN, UNANNOTATED
6. New 'reported' field. A variant will be marked as reported if the filter = PASS and either one or both of the following criteria are met:

• Pathogenicity in ('WHITE_LIST','CLINVAR_PATHOGENIC','CLINVAR_LIKELY_PATHOGENIC')
• Pathogenicity = 'UNANNOTATED' and effect is configured as a known snpeffect

7. Added optional IgnoreEffect XML config list, to ignore effects which are benign, likely benign or unannotated.

The HMF XML config file is attached to this release.

Due to the introduction of the Pathogenic field, the ClinVar filters file now includes all variants matching genes in the HMF config file. The ClinVar filters file can be generated, but is also attached to this release.

sage-v2.2

Changes include:

• Realignment of inframe indels
• Improved MNV deduplication
• Detection of phased inframe indels
• Base Quality Recalibration
• Improved sensitivity in high depth regions
• Tumor only support
• Mitochondria support
• Multiple tumor support
• Multiple reference (or RNA) support
• Removed explicit RNA support (can use additional reference instead)
• Performance and memory improvements

purple-v2.43

• Update allelic frequency calculation
• Fix bug when trying to recover structural variant in alt contig

amber-v3.3

Improvements include:

• Improved contamination check for very shallow sequencing
• Support for multiple references

purple-v2.41

Includes the following changes:

• Fix bug when trying to recover structural variant without allelic frequency
• Fix bug when trying to recover structural variant in alt contig
• Updated fitting deviation to aggressively penalise highly negative implied copy number

sv-linx 1.9

Minor technical changes only:

• check validity of all input files and paths
• removed 'chr' from chromosome name for HG38 support

purple-v2.40

Changes include:

• Increase default value of min_diploid_tumor_ratio_count_centromere to 150
• Update driver catalog DNDS values
• Driver catalog does not run by default. Only if driver_catalog argument supplied
• Driver catalog requires KnownHotspots vcf

linx-v1.8

Functional:

• Visualiser - when specifying a gene to display, this can now be referenced in the Ensembl data cache rather than the more limited internal gene panel by providing a path to the data cache with config: 'gene_transcripts_dir'
• cluster 3 or more overlapping DELs and DUPs with matching copy number and forming potential links
• added INDEL annotation for shattering analysis with config: 'indel_annotation' and 'indel_input_file'
• chain consistency now checks for valid centromere traversal
• re-search for chained foldbacks once chaining is complete
• germline SVs disruption logic added
• Double Minutes:
  • criteria to identify possible BFB ploidy, pairs of SGL breakends
  • allow closed DM loops to amplify centromere
  • check all arms in cluster for telo/centro CN vs DM ploidy or require 50x sample ploidy

Technical

• fail if fusion reference files aren't found, DEV-1121

sage-v2.1

Improvements include:

• Reduced memory footprint
• Add version info to VCF
• RNA support
• CRAM support
• Filter variants with ref containing bases other then G,A,T,C
• Look for read context of variants that are partially soft clipped
• HG38 support