Nextflow-based bioinformatics pipeline for processing tumor sequencing data from tumor-normal pairs to generate variant calls, copy number profiles and other genomic outputs.
Data life cycle
Plan
Collect
Process
Analyse
Preserve
Share
Reuse
Tool information
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Resources
Website
Training
Supporting software
- Nextflow - Workflow orchestration system required to run Oncoanalyser
- Singularity or Docker - Container runtime for reproducible execution
Scripts and workflows
Metadata and data standards
- VCF format - Variant call output format
- MAF format - Mutation annotation format for cancer data
Specific documentation, e.g. versioning
Integrations with other tools
- cBioPortal - Outputs can be converted to cBioPortal format for visualization
