sash is the UMCCR post-processing WGS workflow. The workflow takes DRAGEN small variant calls and oncoanalyser results
as input to perform annotation, prioritisation, rescue and filtering, and reporting for the WGS variant data.
Additionally, sash runs several sensors for biomarker assessment and genomic characterisation including HRD status,
mutational signatures, purity/ploidy, MSI, and TMB.
While the sash workflow utilises a range of tools and software, it is most closely coupled with
bolt, a Python package that implements the UMCCR post-processing logic and supporting
functionality.
The general processes sash runs include:
- gpgr for generating the summary Cancer Report
- PCGR to report processed small somatic variants (annotated, rescued, filtered, prioritised)
- CPSR to report processed small germline variants (filtered, annotated, prioritised)
- linxreport to collate SV annotations and plots from LINX
- MultiQC for reporting various WGS statistics / metrics for QC
- SAGE variant calling to supplement DRAGEN small somatic variants
- PURPLE for TMB, MSI, CNV calling, and purity / ploidy estimation
- HRDetect and CHORD for HRD inference
- MutationalPatterns to fit mutational signatures
- Java
- Nextflow ≥22.10.6
- Docker
Create a samplesheet
id,subject_name,sample_name,filetype,filepath
subject_a.example,subject_a,sample_germline,dragen_germline_dir,/path/to/dragen_germline/
subject_a.example,subject_a,sample_somatic,dragen_somatic_dir,/path/to/dragen_somatic/
subject_a.example,subject_a,sample_somatic,oncoanalyser_dir,/path/to/oncoanalyser/
Execute analysis
nextflow run scwatts/sash \
-profile docker \
--input samplesheet.csv \
--ref_data_path /path/to/reference_data/ \
--outdir output/