Clinical-Genomics/oncorefiner

Introduction

Clinical-Genomics/oncorefiner is a customizable post-processing and extension layer for nf-core/Oncoanalyser that adapts its outputs according to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser's robust core.

1. Process SNV VCF files

   1. Annotate with Vcfanno. Intended for local/custom annotation.
   2. Filter with bcftools. This step aims to apply quality, population-level filtering and/or other general criteria as defined in the configuration settings.
   3. Annotate with Ensembl VEP
   4. Filter with bcftools. This step applies clinically relevant filters as defined in the configuration settings. For example, it may involve subsetting variants based on a a list of clinically relevant genes.

2. Process SV VCF files

   1. Annotate VCF with external database (params) using SVDB.
   2. Filter with bcftools. This step aims to apply quality, population-level filtering and/or other general criteria as defined in the configuration settings.
   3. Annotate with Ensembl VEP.
   4. Filter with bcftools. This step applies clinically relevant filters as defined in the configuration settings. For example, it may involve subsetting variants based on a a list of clinically relevant genes.

3. Present QC for raw reads (MultiQC).

For further information about the each step and output files, please refer to the output documentation.

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,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Note

The information from the samplesheet is not currently used in the pipeline, but it is required to be able to run the pipeline and will be used in future developments.

Now, you can run the pipeline using:

nextflow run Clinical-Genomics/oncorefiner \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

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

Clinical-Genomics/oncorefiner was originally written by Clinical Genomics Stockholm.

We thank the following people for their extensive assistance in the development of this pipeline:

• Beatriz Sá Vinhas
• Eva Caceres
• Kristine Bilgrav Sæther
• Felix Lenner
• Mathias Johansson

Contributions and Support

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

Citations

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.