This repository contains the suite of tools used in the Hartwig Medical Foundation whole genome,targeted DNA and whole transcriptome analysis pipeline.
The latest HMF pipeline is v5.34. Release notes are here.
The table below has links for the each tool used in this release.
The full pipeline can be run using a NextFlow implmentation called OncoAnalyser.
An example WGS pipeline which runs each of these components in turn is detailed here. An example targeted-panel pipeline, including support for the HMF and TSO-500 panels, is detailed here.
| Component | Description | Current Version |
|---|---|---|
| Amber | Generate a tumor BAF file for Purple's copy number fit | 4.0 |
| BamTools | BAM metrics and slicing | 1.2 |
| Cider | TCR/BCR V(D)J recombination sequence detection | 1.0.3 |
| Cobalt | Determines the read depth ratios for Purple's copy number fit | 1.16 |
| Cuppa | Tissue of origin prediction from WGS/WTS | 2.0 |
| Gripss | SV filtering | 2.4 |
| Lilac | HLA typing | 1.6 |
| Linx | SV annotation, clustering & chaining, fusion and disruption calling | 1.25 |
| MarkDups | Duplicate marking, consensus reads, UMIs and read unmapping | 1.1 |
| Pave | Point mutation annotation and gene impact | 1.6 |
| Purple | Estimates copy number, purity and ploidy, and identifies driver events | 4.0 |
| Sage | Point mutation variant calling and filtering | 3.4 |
| Teal | Measures telomere content and estimates telomeric length | 1.2.1 |
| SvPrep | Pre-GRIDSS BAM filtering | 1.2 |
The following external tools are used in the pipeline:
| Component | Description | Current Version |
|---|---|---|
| GRIDSS | Structural variant calling | 2.13.2 |
| Chord | Homologous Recombination Deficiency detection | 2.0 |
Resource files for each component (GRCh37 and GRCh38) are available to download from HMFTools-Resources > DNA-Resources.
| Component | Description | Current Version |
|---|---|---|
| Protect | Matching of molecular results to treatments and clinical trials | 2.3 |
| Rose | Actionability of clinically relevant molecular findings | 1.3 |
| Virus Interpreter | Filtering, annotation and interpretation of virus breakend data | 1.3 |
| Orange | PDF summary report and JSON file of all WGS output | 3.2.0 |
| Patient-reporter | PDF summary report and JSON file of all clinical relevant WGS output | 7.25.1 |
| Component | Description | Current Version |
|---|---|---|
| Isofox | WTS Transcript Abundance, Fusions & Novel Splice Junctions | 1.7 |