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This is a genomics pipeline to do a single germline sample variant-calling, adapted from GATK Best Practice Workflow.

This workflow is a reference pipeline for using the Janis Python framework (pipelines assistant).

  • Alignment: bwa-mem
  • Variant-Calling: GATK HaplotypeCaller
  • Outputs the final variants in the VCF format.


This pipeline has been tested using the HG38 reference set, available on Google Cloud Storage through:

Type: Janis

Creators: Richard Lupat, Michael Franklin; Jiaan Yu; Juny Kesumadewi

Submitter: Richard Lupat

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