Somatic copy number alteration (SCNA) pattern identification in shallow whole-genome sequencing data

Introduction

dincalcilab/scnapattern is a bioinformatics pipeline that assigns somatic copy number alterations (SCNA) patterns (S, stable; U, unstable; HU, highly unstable) as described in Copy number alterations in stage I epithelial ovarian cancer highlight three genomic patterns associated with prognosis by Pesenti, Beltrame, et al.

This pipeline requires shallow whole-genome sequencing (sWGS) data with absolute copy number and ploidy estimates. Currently segmentation outputs from ASCAT.sc, ACE, and ichorCNA are supported natively.

The pipeline includes these steps:

1. Calculate SCNA patterns for given inputs
2. Output a table with patterns and parameters for each analyzed sample
3. Generate a QC summary (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,filename,ploidy,format
Sample_1,Sample1.cna.seg,2,ichorcna

Each row represents a sample name, the associated absolute path to the segment file, the ploidy of the sample, and the data format (either ascat, ace, or ichorcna).

Now, you can run the pipeline using:

nextflow run dincalcilab/scnapattern \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR> \
   --genome <GENOME> \
   --genomestyle <GENOMESTYLE>

Where GENOME is either hg19 or hg38 and genomestyle is either ucsc (chr prefix for chomosomes) or ncbi (no chr prefix). Note that you must use a Nextflow configuration profile that supports Docker or Singularity images, as some tools are only provided by containers.

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.

Credits

dincalcilab/scnapattern was originally written by Luca Beltrame (@lbeltrame).

Contributions and Support

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

Citations

If you use dincalcilab/scnapattern for your analysis, please cite it using the following doi: 10.1016/j.ejca.2022.05.005

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.