WiGiTS is a universal open source suite of genome and transcriptome analysis tools for cancer research and diagnostics
![image](https://private-user-images.githubusercontent.com/18154939/342965534-187fe7be-6ad4-4e1f-8fff-96b0a06cadbd.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.7ZRuc7R7GN3mySjUcdhwGamyYusfmivD77ut55B3DZM)
We recommend to run WiGiTS using the NextFlow implmentation called OncoAnalyser.
Alternatively, 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.
Here is a schematic showing how the interactions between the core molecular DNA components of the tool suite:
The latest HMF pipeline is v5.34. Release notes are here.
The table below has links for the each tool used in this release.
Component | Description | Current Version |
---|---|---|
Amber | Generate a tumor BAF file for Purple's copy number fit | 4.0.1 |
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 | 2.1.1 |
Gripss | SV filtering | 2.4 |
Lilac | HLA typing | 1.6 |
Linx | SV annotation, clustering & chaining, fusion and disruption calling | 1.25 |
Pave | Point mutation annotation and gene impact | 1.6 |
Purple | Estimates copy number, purity and ploidy, and identifies driver events | 4.0 |
Redux | Duplicate marking, consensus reads, UMIs and read unmapping | 1.1.7 |
Sage | Point mutation variant calling and filtering | 3.4 |
Teal | Measures telomere content and estimates telomeric length | 1.3.0 |
SvPrep | Pre-GRIDSS BAM filtering | 1.2.3 |
The following external tools are also used in the pipeline:
Component | Description | Current Version |
---|---|---|
GRIDSS | Structural variant calling | 2.13.2 |
Chord | Homologous Recombination Deficiency detection | 2.0 |
Component | Description | Current Version |
---|---|---|
Isofox | WTS Transcript Abundance, Fusions & Novel Splice Junctions | 1.7 |
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 | 3.5.0 |
Patient-reporter | PDF summary report and JSON file of all clinical relevant WGS output | 7.25.1 |
Resource files for each component (GRCh37 and GRCh38) are available to download from HMFTools-Resources > DNA-Resources.