Pipeline for RNA and DNA integrated analysis for somatic mutation detection
The nf-core/rnadnavar is a bioinformatics best-practice analysis pipeline for RNA somatic mutation detection able to perform in parallel.
Initially designed for cancer research, the pipeline uses different variant calling algorithms and applies a consensus approach. A final filtering stage, should provide a set of annotated somatic variants.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
Depending on the options and samples provided, the
pipeline will run different tasks. This is controlled
--tools parameters. This
is a summary of the possible tasks to run with the pipeline:
- Quality control and trimming (enabled by
- Map Reads to Reference (BWA-mem, BWA-mem2, dragmap and/or STAR)
- GATK preprocessing for DNA and RNA bulk sequencing
- Summarise alignment statistics (
- Variant calling (enabled with
- Annotation with
- Normalisation of VCFs with VT (enabled with
- Transformation of VCF to MAF and consensus of variant
calling results (enabled with
- Filtering of MAF files applying optional gnomad,
whitelisting and blacklisting (enabled with
- Realignment step where reads from regions where a variant
was found will be extracted and re-processed, only for
RNA due to higher levels of background noise (enabled
- Filtering of MAF files specific for RNA (enabled with
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.
The nf-core/rnadnavar was originally written by Raquel Manzano Garcia at Cancer Research UK Cambridge Institute with the continuous support of Maxime U Garcia. The workflow is based on RNA-MuTect which was originally published by Yizhak, et al 2019 (Science)
We thank the following people for their assistance in the development of this pipeline: TBC
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.