nf-core pipeline ·
nf-core/variantprioritization
Functional annotation and clinical interpretation of somatic and germline cancer variants using PCGR and CPSR.
What nf-core/variantprioritization is
nf-core/variantprioritization is a bioinformatics analysis pipeline designed for the functional annotation and interpretation of cancer variants. It translates somatic single nucleotide variants (SNVs), small insertions and deletions (InDels), and copy number aberrations into clinical reports using the Personal Cancer Genome Reporter (PCGR). Additionally, the pipeline interprets and annotates germline SNVs and InDels using the Cancer Predisposition Sequencing Reporter (CPSR).
The pipeline was originally developed by Barry Digby, Youssef Abili, and Matteo Bonfanti, with contributions from Fabio Malcher Miranda to align the pipeline with nf-core standards. It was specifically designed to ingest and interpret variant calling outputs produced by nf-core/sarek.
What the pipeline does
The workflow reads a comma-separated samplesheet specifying patient identifiers, sample tumour-normal status, sample identifiers, VCF paths, and optional copy number aberration (CNA) segment files. Germline variants derived from callers such as DeepVariant or HaplotypeCaller are routed to CPSR for cancer predisposition reporting. Somatic SNVs and InDels from callers like Mutect2 and Strelka, along with copy number segments from ASCAT, are processed through PCGR for somatic oncology reporting. When CNA analysis is activated, segment files must be supplied for every sample entry in the samplesheet.
Key facts
- Pipeline engine
- Nextflow
- Primary annotation tools
- PCGR, CPSR
- Upstream compatibility
- nf-core/sarek
- Supported somatic callers
- Mutect2, Strelka, ASCAT
- Supported germline callers
- DeepVariant, HaplotypeCaller
- Input file formats
- CSV (samplesheet), VCF, CNA segment text files
- Latest release
- 1.0.0 (2026-04-09)
What you can use it for
- Somatic variant interpretation
- Annotating and translating somatic SNVs and InDels from tumour-normal or tumour-only sequencing experiments using PCGR.
- Germline cancer predisposition screening
- Evaluating patient germline variants with CPSR to detect hereditary cancer predisposition alterations.
- Integrated copy number and SNV reporting
- Combining ASCAT segment profiles with somatic point mutation data for simultaneous interpretation in PCGR.
- Post-processing nf-core/sarek outputs
- Directly interpreting outputs from nf-core/sarek variant calling runs using compatible sample sheet configurations.
Run it here
The research agent runs nf-core/variantprioritization with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Processes both somatic and germline variant data using dedicated reporting engines (PCGR and CPSR).
- Accepts direct output file structures from the nf-core/sarek pipeline.
- Supports combined analysis of small sequence variants and somatic copy number aberrations.
Watch out for
- The Conda profile (-profile conda) is currently incompatible with the PCGR and CPSR pipeline modules.
- Pipeline parameters cannot be supplied through custom configuration files passed with the -c Nextflow option.
- CNA segment files must be supplied for all sample entries when CNA analysis is enabled.
Questions
Can I run nf-core/variantprioritization without my own cluster?
The research agent runs nf-core/variantprioritization with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/variantprioritization under?
MIT, like every nf-core pipeline.
Which upstream variant callers are supported?
The pipeline supports germline calls from DeepVariant and HaplotypeCaller, somatic point mutations and InDels from Mutect2 and Strelka, and copy number aberration segments from ASCAT.
Can the pipeline be run using Conda?
No, running with -profile conda is currently not supported due to issues with the CPSR and PCGR modules.
How are pipeline parameters configured?
Parameters must be supplied via the command-line interface or using a Nextflow -params-file option, as custom configuration files provided via -c cannot specify pipeline parameters.
Is copy number aberration data mandatory?
Copy number aberration files are only mandatory for all sample entries when the parameter --cna_analysis is set to true.
How to cite it
doi: 10.5281/zenodo.19480994
Written from nf-core/variantprioritization's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.