Generate Panel of Normals, models or other similar references from lots of samples
nf-core/createpanelrefs is a bioinformatics helper pipeline that will help in creating panel of normals and other models.
- Read QC (
- Build Panel of Normals for
- Build ploidy and cnv calling models for
GATK's germlinecnvcaller workflow
- Present QC for raw reads (
First, prepare a samplesheet with your input data that looks as follows:
Each row in the samplesheet represents an alignment file, and it is important that you provide the files in the right format for the analysis you want to run.
|bam or cram or a mix of both
Now, you can run the pipeline using:
Please provide pipeline parameters via the CLI or Nextflow
-params-file option. Custom config files including those provided by the
-c Nextflow option can be used to provide any configuration except for parameters;
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
nf-core/createpanelrefs was originally written by @maxulysse. @marrip contributed in the idea that started it all. @matthdsm and @FriederikeHanssen contributed in the actual design. @ramprasadn’s interest was the final push that led to the creation.
We thank the following people for their extensive assistance in the development of this pipeline:
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
An extensive list of references for the tools used by the pipeline can be found in the
You can cite the
nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.