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Beta release of precision medicine analysis-workflows

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@jasonwalker80 jasonwalker80 released this 28 Feb 20:04
· 1422 commits to master since this release
v1.4-beta.1
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This is a beta release of workflows for enabling precision medicine to perform neoantigen predictions and subsequent personalized cancer vaccine designs.

Improvements

  • Reorganized code into tools, sub-workflows and pipelines.
  • Increase the use of task-specific docker images
  • Additional and updated ResourceRequirements
  • Numerous QC tools added for WGS, Exome and RNA-seq
  • Structural Variant and Copy Number calls, ex. Lumpy/smoove, Manta, CNVkit
  • Additional annotation: custom ClinVar, VEP --everything
  • Option to limit variant calls to defined regions, ex. ACMG genes
  • Numerous other changes to the order of steps, secondary files and exposure of tool parameters to the workflows.

Pipelines Supported

  • Somatic WGS and Exome
  • Germline WGS and Exome
  • scRNA-seq and RNA-seq Expression/Abundance Estimates
  • Whole-Genome Bisulfite (WGBS)
  • pVACseq for neoantigen predictions
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