SuSiE Fine-Mapping Workflow
| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
|---|---|---|---|
| aou_9.0.1 | January, 2026 | WARP Pipelines | File an issue |
Introduction to the SuSiE Fine-Mapping workflow
susieR_workflow.wdl performs cis-window fine-mapping using SuSiE from TensorQTL outputs and dosage matrices.
The workflow subsets phenotype/genotype inputs for a target phenotype ID, then runs an R-based SuSiE script to produce parquet outputs including credible set summaries and full fine-mapping tables.
Inputs
Input descriptions
| Input variable name | Description | Type |
|---|---|---|
GenotypeDosages | BGZ-compressed dosage matrix. | File |
GenotypeDosageIndex | Tabix index for dosage matrix. | File |
QTLCovariates | Covariate table for QTL model fitting. | File |
TensorQTLPermutations | TensorQTL permutation output table used to select phenotype-specific loci. | File |
SampleList | Sample metadata file. | File |
PhenotypeBed | Phenotype BED matrix used for expression/splicing values. | File |
CisDistance | Cis-window distance parameter. | Int |
susie_rscript | SuSiE runner script path. | File |
memory | Runtime memory (GB). | Int |
NumPrempt | Runtime preemptible count. | Int |
OutputPrefix | General output prefix. | String |
PhenotypeID | Target phenotype ID for subsetting and fine-mapping. | String |
Outputs
| Output variable name | Filename, if applicable | Output format and description |
|---|---|---|
SusieParquet | <PhenotypeID>.parquet | Primary SuSiE fine-mapping parquet output. |
SusielbfParquet | <PhenotypeID>.lbf_variable.parquet | Variant-level log-Bayes-factor parquet output. |
FullSusieParquet | <PhenotypeID>.full_susie.parquet | Expanded full SuSiE results parquet. |
SubsetBed | <PhenotypeID>.bed.bgz | Phenotype-specific subset bed used during run. |
SubsetDosages | <PhenotypeID>.dose.tsv.gz | Dosage matrix subset for selected phenotype interval. |
SubsetDosagesIndex | <PhenotypeID>.dose.tsv.gz.tbi | Tabix index for SubsetDosages. |
Workflow and WDL
- Workflow:
susieR_workflow - Source WDL:
susieR_workflow.wdl
Versioning
All susieR_workflow 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.