GVS AoU Reblock gVCF
| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
|---|---|---|---|
| aou_9.0.0 | August, 2025 | WARP Pipelines | File an issue |
Introduction to the GVS AoU Reblock gVCF workflow
GvsAoUReblockGvcf reblocks existing per-sample gVCFs using GATK ReblockGVCF and optionally copies results to site-specific AoU research buckets.
This workflow is commonly used as a preparation step before external joint calling systems (e.g., GVS-based aggregation workflows).
Quickstart table
| Pipeline Feature | Description | Source |
|---|---|---|
| Analysis type | gVCF reblocking and optional site-bucket copy | |
| Workflow language | WDL 1.0 | openWDL |
| Data input file format | gVCF path + reference bundle | |
| Data output file format | Reblocked gVCF + index | |
| Primary software | GATK ReblockGVCF + gsutil | GATK |
Set-up
GVS AoU Reblock gVCF installation and requirements
The workflow code can be downloaded by cloning the WARP GitHub repository. For the latest release, please see the GvsAoUReblockGvcf changelog.
The pipeline can be deployed using Cromwell, a GA4GH-compliant workflow management system.
Inputs
Input descriptions
| Input variable name | Description | Type |
|---|---|---|
gvcf | GCS path to input gVCF (.g.vcf.gz). | String |
gvcf_index | (Optional) Index path for input gVCF. Defaults to gvcf + ".tbi". | String? |
ref_dict | Reference sequence dictionary. | File |
ref_fasta | Reference FASTA. | File |
ref_fasta_index | FASTA index. | File |
requester_pays_project | (Optional) GCS requester-pays project passed to GATK. | String? |
site_id | (Optional) Destination site code (bi, bcm, uw). | String? |
docker_image | Docker image for GATK ReblockGVCF. Default: us.gcr.io/broad-gatk/gatk:4.2.6.1. | String |
GVS AoU Reblock gVCF tasks and tools
This workflow runs a single task.
| Task name and WDL link | Tool | Software | Description |
|---|---|---|---|
| ReblockAndCopy | GATK ReblockGVCF | configurable (docker_image) | Reblocks input gVCF, then optionally copies output and index to a site-specific bucket prefix. |
1. Reblock and optionally copy output
ReblockAndCopy runs GATK with fixed GQ bands and optional requester-pays settings. If site_id is provided, output files are copied to the mapped destination bucket path.
Outputs
| Output variable name | Filename, if applicable | Output format and description |
|---|---|---|
reblocked_gvcf | <basename>.reblocked.g.vcf.gz | Reblocked gVCF output (optionally delocalized to site-specific bucket path). |
reblocked_gvcf_index | <basename>.reblocked.g.vcf.gz.tbi | Tabix index for reblocked gVCF. |
Versioning
All GvsAoUReblockGvcf releases are documented in the changelog.
Feedback
Please help us make our tools better by filing an issue in WARP; we welcome pipeline-related suggestions or questions.