HLA Genotyping Workflows (WDL)
This section documents the All of Us HLA workflows for per-sample HLA calling and cohort-level aggregation.
Quick Summary
- Purpose: Perform HLA genotyping from aligned sequencing data and aggregate per-sample consensus calls.
- Primary Outputs: Per-sample consensus HLA calls and combined cohort-level tables.
Workflow Overviews
| Step | Workflow | Description | WDL |
|---|---|---|---|
| 1 | HLA Consensus Genotyping | Extracts HLA reads, runs HLA-HD with conditional Polysolver/OptiType fallback, and emits consensus calls. | WDL |
| 2 | HLA Make Table | Combines per-sample consensus calls into a cohort-level result table. | WDL |
Suggested Usage Pattern
- Run
HLAGenotypingper sample. - Collect consensus outputs and run
MakeTablefor cohort aggregation.
Feedback
Please help us make our tools better by filing an issue in WARP; we welcome pipeline-related suggestions or questions.