nf-core pipeline ·
nf-core/createpanelrefs
Builds panels of normals and reference models for copy number and variant calling tools from multiple samples.
What nf-core/createpanelrefs is
nf-core/createpanelrefs is a bioinformatics helper pipeline designed to construct Panel of Normals (PoN) datasets, ploidy models, and other reference baselines from cohort sequencing data. In genomic analyses, reference panels of normal samples are used to distinguish true biological variants from technical artefacts, sequencing noise, and cohort-level biases.
The pipeline generates reference assets for several downstream somatic and germline analysis tools, including CNVkit, GATK GermlineCNVCaller, GENS, and Mutect2. It also integrates sample read evaluation via FastQC and summarises analytical metrics across the cohort using MultiQC.
Originally authored by Maxime Ulysse Garcia with contributions and design input from members of the nf-core community, the pipeline standardises reference creation workflows within Nextflow.
What the pipeline does
The workflow ingests a comma-separated samplesheet defining sample identifiers and aligned sequence files in BAM or CRAM formats, along with their respective index files (BAI or CRAI). Users specify target tools and genome builds through execution parameters.
Depending on the selected targets, the pipeline executes quality assessment on reads with FastQC, processes BAM alignments to produce CNVkit reference panels, builds ploidy and copy number calling models for GATK GermlineCNVCaller, and creates panels of normals for GENS and Mutect2. Output reports and run summaries are aggregated via MultiQC.
Key facts
- Pipeline engine
- Nextflow
- Latest release
- 1.0.0 (2026-06-08)
- Input formats
- BAM, BAI, CRAM, CRAI (via CSV samplesheet)
- Supported tools
- CNVkit, GATK GermlineCNVCaller, GENS, Mutect2, FastQC, MultiQC
- Original author
- Maxime Ulysse Garcia (@maxulysse)
What you can use it for
- CNVkit panel generation
- Build a pooled normal reference file from a cohort of BAM alignments for subsequent copy number variation calling in CNVkit.
- GATK germline CNV model creation
- Generate ploidy models and copy number calling models required by the GATK GermlineCNVCaller workflow using BAM, CRAM, or mixed alignment inputs.
- Mutect2 Panel of Normals construction
- Compile a Panel of Normals from sequencing alignments to filter false positives and recurrent artefacts in Mutect2 somatic variant detection.
- GENS reference panel preparation
- Produce normal reference files used for copy number profile visualisation and analysis within the GENS application.
Run it here
The research agent runs nf-core/createpanelrefs 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
- Consolidates reference panel generation across multiple distinct variant and copy number calling tools into a single pipeline.
- Accepts BAM, CRAM, or mixed alignment formats when constructing GATK GermlineCNVCaller models.
- Automates read-level and cohort-level quality control reporting through integrated FastQC and MultiQC modules.
Watch out for
- CNVkit reference generation requires BAM alignments and does not accept CRAM files.
- Pipeline configuration parameters must be supplied via the command line or parameter files, as custom configuration files cannot define parameters.
Questions
Can I run nf-core/createpanelrefs without my own cluster?
The research agent runs nf-core/createpanelrefs 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/createpanelrefs under?
MIT, like every nf-core pipeline.
What alignment formats does the pipeline accept?
The pipeline accepts BAM and CRAM files along with their matching index files (BAI and CRAI), recorded in a CSV samplesheet.
Can CRAM files be supplied for CNVkit panel creation?
No. CNVkit requires alignments in BAM format, whereas GATK GermlineCNVCaller accepts BAM, CRAM, or a combination of both.
Which downstream tools are supported for reference generation?
The pipeline supports reference panel and model generation for CNVkit, GATK GermlineCNVCaller, GENS, and Mutect2.
How is quality assessment reported?
Read quality control is evaluated using FastQC, and the resulting metrics are compiled into an aggregated MultiQC report.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/createpanelrefs's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.