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Janis1
Submitter
Richard Lupat1
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Janis1
Space
Australian BioCommons1
Creator
Richard Lupat1
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Work-in-progress1
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Work-in-progress
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.
Resources
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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