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D3b RNAseq SNV Calling Workflow (beta)

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@migbro migbro released this 17 Apr 19:44
· 32 commits to master since this release
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Learn about vigilant mode.

This repo contains RNAseq SNV calling pipelines using:

  • Broad GATK4 best practices
    • The overall workflow picks up from post-STAR alignment, starting at Picard mark duplicates.
    • For the most part, tool parameters follow defaults from the GATK Best Practices WDL, written in cwl with added optimatization for use on the Cavatica platform.
  • Strelka2
    • This workflow is pretty straight forward, with a PASS filter step added to get PASS calls.
  • VarDict Java
    • This workflow is based on the Vardict run style of BC Bio.
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