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Integrate DRAGEN-SV into pipeline #749

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@kjaisingh kjaisingh commented Nov 20, 2024

Description

This PR is intended to integrate DRAGEN-SV into the GATK-SV pipeline. It introduces several changes, including but not limited to:

  • Adds DRAGEN-SV parameters to WDLs that process and/or analyze caller-specific VCFs.
  • Extends make_evidence_qc_table.py to include tests on raw DRAGEN-SV VCFs.
  • Introduces std_dragen.py that enables standardizing of raw DRAGEN-SV VCFs.
  • Modifies MakeGqRecalibratorTrainingSetFromPacBio to only optionally require VCFs from all callers.

Testing

  • (TODO) This Terra job shows an example run of the pipeline prior to this change.
  • (TODO) This Terra job shows an example run of the pipeline with this change.
  • Validated all WDLs with womtool.

Pre-Merge Changes Required

Remove automated syncing of WDLs to Dockstore.

@kjaisingh kjaisingh self-assigned this Nov 20, 2024
@kjaisingh kjaisingh added the enhancement New feature or request label Nov 20, 2024
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