Pipeline v5.33 Release Notes
Summary of improvements:
-
RefSeq gene annotations:
Variants in certain genes are now annotated with RefSeq transcript IDs in addition to the Ensembl transcript IDs. -
Improved targeted panel analysis:
Various tools contain updates to support targeted panel analysis better.
Detailed Tool Changes
| Component | Version | Key Functional Changes |
|---|---|---|
| Purple | 3.9 | Various panel changes, add somatic likelihood |
| Sage | 3.3 | Track UMI counts, Gene coverage to min map quality >= 10, minor panel filtering changes |
| Pave | 1.5 | Phased variant fixes |
| Cobalt | 1.15.2 | Panel GC refinements & fixes |
| BamTools | 1.1 | Exclude duplicates from fragment length distribution |
| MarkDups | 1.0 | Initial version with read consensus & UMIs |
| Linx | 1.24.1 | Visualiser improvements and fusion plot fixes |
| Lilac | 1.5 | Output as TSV |
| PatientDB | 5.33 | Add Clinvar, Gnomad and Somatic Likelihood to somatic variant table |
| Cuppa | 1.8.1 | Alternative SJ fix for RNA samples |
| Health-Checker | 3.5 | Compatibility with samtools Flagstats (instead of from Sambamba) |
| Virus Interpreter | 1.3 | Use updated virus enumerations |
| Orange | 2.6.0 | Support non standard transcripts from PURPLE vcf |
| Chord | 2.02 | Require 100 INDELs or 30 SVs to make a prediction, as opposed to 50 INDELs or 30 SVs before |
Changes to resource files
| File | Tool | Change |
|---|---|---|
| Driver gene panel | Many | Several germline genes added |
| CoverageCodingPanel | Sage | All driver panel genes included |
| Ensembl data cache | Pave | RefSeq transcripts added |
| Fusions | Linx | FGFR1 HighImpactPromiscuous back to false |
| Clinvar | Pave | Updated to latest |
| KnownGermlineHotspots | Sage | Following Clinvar update |
| KnownSomaticHotspots | Sage | Six manually curated hotspots added |
| HMF targeted panel files | Purple, Cobalt | Normalisation to use 64 samples, TMB calc adjustments |
| Old Gridss resource files | Gridss | Deleted/cleaned up |