NCI-CGR / GEMSCAN

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

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
• Technical Lead: Bin Zhu

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 nci-cgr.github.io/gemscan/

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.
3. Commit and push your changes to your fork.
4. Create a pull request against the original repository.