This pipeline was set up to test a variety of CNV calling tools on WES and WGS samples sequenced using Illumina short-read sequencing technology.
This pipeline is set up as a Snakemake workflow. More information on how to install and run Snakemake can be found at the wiki.
After installation of Snakemake, clone this repository and fill in the config.yaml.
This pipeline is set up to work with the Environment Modules. It likely needs customisation or removal of the module statements in the rules (tools/*/rules.smk) for compatilibility with a given computational environment.
Some of the tools in this pipeline requires a panel of normals, which the pipeline does not generate automatically. One such tool is GATK GermlineCNVCaller. More info on generating a panel of normals for this tool can be found at the GATKs tool documentation
Once the pipeline has been configured, a given tool can be run using the command snakemake $tool.
A list of available Snakemake targets can be generated by running snakemake --list-target-rules.
By default, Snakemake runs all the tools specified in the config.yaml by just running: snakemake.
Many options are available for customizing snakemake behaviour. These are all documented at the Snakemake Wiki.
The alignment file GB-WGS-NA12878.bam used in this project is available at the NCBI Sequencing Read Archive (SRA).
