Integrate DRAGEN-SV into pipeline #749
Draft
+387
−127
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
This PR is intended to integrate DRAGEN-SV into the GATK-SV pipeline. It introduces several changes, including but not limited to:
make_evidence_qc_table.py
to include tests on raw DRAGEN-SV VCFs.std_dragen.py
that enables standardizing of raw DRAGEN-SV VCFs.MakeGqRecalibratorTrainingSetFromPacBio
to only optionally require VCFs from all callers.Testing
Pre-Merge Changes Required
Remove automated syncing of WDLs to Dockstore.