Introduction

qbic-pipelines/createpanelofnormals is a bioinformatics pipeline for creating a panel of normals for Mutect2 following these instructions and CNVKit using cnvkit batch.

1. Variant calling on normal samples with (GATK4 Mutect2)
2. Create GenomicsDB
3. Combine normal calls with CreateSomaticPanelOfNormals
4. Group all normal files and run CNVKit batch with the parameters -n, -t, -m, and -y if (--assume_male is set).

Disclaimer: not tested for panel or exome data. There might be need for more flags or input files.

3. Collect versions in (MultiQC)

Usage

Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,cram,crai
sample1,test.cram,test.cram.crai

Each row represents one sample.

Now, you can run the pipeline using:

nextflow run qbic-pipelines/createpanelofnormals \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

To get an overview over all available parameters, run:

nextflow run qbic-pipelines/createpanelofnormals --help

Warning: 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; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

For more details about the output files and reports, please refer to the output documentation.

Credits

qbic-pipelines/createpanelofnormals was originally written by FriederikeHanssen.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch by opening an issue.

Citations

If you use qbic-pipelines/createpanelofnormals for your analysis, please cite it using the following doi: 10.5281/zenodo.671039381

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

The pipeline is currently maintained at QBiC and not an nf-core pipeline since it has not undergone nf-core community review. It was created using the nf-core template and integrates their institutional profiles as well as many other resources. If you use this pipeline, please cite them 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.