GEMSCAN - GErMline Snp Small Indel CAller PipeliNe

Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.

Authors

• Shalabh Suman, Bari Ballew and Wendy Wong

Usage

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and, if available, its DOI (see above). The documentation of this pipeline is at https://gemscan.readthedocs.io/en/latest/

Step 1: Obtain a copy of this workflow

1. Clone this repository to your local system, into the place where you want to perform the data analysis.

    git clone ______

Step 2: Configure workflow

Configure the workflow according to your needs via editing the files in the config/ folder. Adjust config.yaml to configure the workflow execution, and manifest.tsv to specify your sample setup.

Step 3: Install Snakemake

Install Snakemake using conda:

conda create -c bioconda -c conda-forge -n snakemake snakemake

For installation details, see the instructions in the Snakemake documentation.

Step 4: Execute workflow

Activate the conda environment:

conda activate snakemake

Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores $N

using $N cores or run it in a cluster environment via

snakemake --use-singularity --cluster qsub --jobs 100

run it with google lifesciences pipeline via (note that the --google-lifesciences does not support singularity)

export GOOGLE_APPLICATION_CREDENTIALS="path/to/your/credentials.json"
snakemake --google-lifesciences --default-remote-prefix <googleBucketForOutputs> --use-conda  --jobs 100

See the Snakemake documentation for further details.

Step 5: Investigate results

Step 6: Commit changes

Whenever you change something, don't forget to commit the changes back to your github copy of the repository:

git commit -a
git push

Step 7: Obtain updates from upstream

Whenever you want to synchronize your workflow copy with new developments from upstream, do the following.

1. Once, register the upstream repository in your local copy: git remote add -f upstream git@github.com:snakemake-workflows/germlineSmallVariantCallingV4.git or git remote add -f upstream https://github.com/snakemake-workflows/germlineSmallVariantCallingV4.git if you do not have setup ssh keys.
2. Update the upstream version: git fetch upstream.
3. Create a diff with the current version: git diff HEAD upstream/master workflow > upstream-changes.diff.
4. Investigate the changes: vim upstream-changes.diff.
5. Apply the modified diff via: git apply upstream-changes.diff.
6. Carefully check whether you need to update the config files: git diff HEAD upstream/master config. If so, do it manually, and only where necessary, since you would otherwise likely overwrite your settings and samples.

Step 8: Contribute back

In case you have also changed or added steps, please consider contributing them back to the original repository:

1. Fork the original repo to a personal or lab account.
2. Clone the fork to your local system, to a different place than where you ran your analysis.
3. Copy the modified files from your analysis to the clone of your fork, e.g., cp -r workflow path/to/fork. Make sure to not accidentally copy config file contents or sample sheets. Instead, manually update the example config files if necessary.
4. Commit and push your changes to your fork.
5. Create a pull request against the original repository.

Testing

Test cases are in the subfolder tests. They are automatically executed via continuous integration (TBD).