Research Object Crate for Janis Germline Variant-Calling Workflow (GATK)

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: - https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/ This pipeline expects the assembly references to be as they appear in that storage (".fai", ".amb", ".ann", ".bwt", ".pac", ".sa", "^.dict"). The known sites (snps_dbsnp, snps_1000gp, known_indels, mills_indels) should be gzipped and tabix indexed. Infrastructure_deployment_metadata: Spartan (Unimelb)

Author

Richard Lupat, Michael Franklin; Jiaan Yu; Juny Kesumadewi

License

Apache-2.0

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