rhshah/caw

Cancer Analysis Workflow: a complete open source pipeline to detect somatic variants from WGS data

Cancer Analysis Workflow

CAW is a complete open source pipeline to detect somatic variants from WGS data developed at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden and National Bioinformatics Infastructure Sweden at SciLifeLab.

The pipeline uses Nextflow, a bioinformatics domain specific language for workflow building and Singularity, a container technology specific for high-performance computing.

This pipeline is primarily used with cluster on the Swedish UPPMAX systems. However, the pipeline should be able to run on any system that supports Nextflow. The pipeline comes with some configuration for different systems. See the documentation for more information.

We utilize GATK best practices to align, realign and recalibrate short-read data in parallel for both normal and tumor sample. After these preprocessing steps, several somatic variant callers scan the resulting BAM files: MuTect1, MuTect2 and Strelka are used to find somatic SNVs and small indels, also GATK HaplotyeCaller for both the normal and the tumor sample. For structural variants we use Manta. Furthermore, we are applying ASCAT to estimate sample heterogeneity, ploidy and CNVs.

The pipeline can begin the analysis either from raw FASTQ files, only from the realignment step, or directly with any subset of variant callers using recalibrated BAM files. At the end of the analysis the resulting VCF files are merged to facilitate further downstream processing, though results from each caller are also retained. The flow is capable of accommodating additional variant calling software or CNV callers. It is also prepared to process normal, tumor and several relapse samples.

Besides variant calls, the workflow provides quality controls presented by MultiQC.

The containers directory contains building rules for containers for all CAW processes.

This pipeline is listed on Elixir - Tools and Data Services Registry.

Documentation

The CAW pipeline comes with documentation about the pipeline, found in the doc/ directory:

1. Installation documentation
2. Installation documentation specific for milou
3. Installation documentation specific for bianca
4. Tests documentation
5. Reference files documentation
6. Configuration and profiles documentation
7. Intervals documentation
8. Running the pipeline
9. Examples
10. TSV file documentation
11. Processes documentation
12. Documentation about containers
13. Documentation about building
14. More information about ASCAT
15. Folder structure

For further information/help contact: [email protected], [email protected] or join the gitter chat: gitter.im/SciLifeLab/CAW.

Authors

• Sebastian DiLorenzo
• Jesper Eisfeldt
• Maxime Garcia
• Szilveszter Juhos
• Max Käller
• Malin Larsson
• Marcel Martin
• Björn Nystedt
• Pall Olason
• Pelin Sahlén

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