Challenging Medically Relevant Genes Variant Calling Workflows (WDL)
This section documents the All of Us CMRG workflows for remapping/calling in difficult regions and reblocking gVCFs for downstream joint analysis.
Quick Summary
- Purpose: Improve variant calling in challenging medically relevant genes and prepare outputs for downstream aggregation.
- Primary Outputs: Corrected-region VCF/gVCF files and reblocked gVCFs.
Workflow Overviews
| Step | Workflow | Description | WDL |
|---|---|---|---|
| 1 | FixItFelix and Variant Calling | Subsets CMRG-relevant reads, remaps to masked GRCh38 using FixItFelix, and runs HaplotypeCaller. | WDL |
| 2 | GVS AoU Reblock gVCF | Reblocks per-sample gVCFs and optionally copies outputs into AoU site-specific research buckets. | WDL |
External Downstream Joint Calling
Joint calling can be performed with external GVS workflows, such as:
Suggested Usage Pattern
- Run FixItFelix remapping + variant calling (
FixItFelixAndVariantCall). - Reblock gVCFs (
GvsAoUReblockGvcf) as needed for storage/joint analysis. - Ingest and joint-call using external GVS pipelines.
Feedback
Please help us make our tools better by filing an issue in WARP; we welcome pipeline-related suggestions or questions.