SuSiE Fine-Mapping Workflow
| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
|---|---|---|---|
| aou_9.1.0 | August, 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.
Given an InputMappingTsv (one row per ancestry) and a target Ancestry, the workflow first looks up the ancestry-specific genotype dosage, covariate, sample list, phenotype BED, and TensorQTL permutation file paths, subsets those 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 |
|---|---|---|
InputMappingTsv | Tab-separated file, one row per ancestry, providing gs:// paths for GenotypeDosage, GenotypeDosagei, PhenotypePCsOut, PlinkAF, QtlCovariates, Sample_list, VCF, cis_qtl, genotype_pcs, pgen, phenotype_bed, and psam, keyed by a mapping_inputs_id ancestry code (AFR, AMR, COMB, EUR, SAS, EAS, MID). | File |
Ancestry | Ancestry code used to select the row of InputMappingTsv to use for this run. | String |
CisDistance | Cis-window distance parameter. | Int |
susie_rscript | SuSiE runner script path; see 20251210_rfast_removed_susie.R in warp-tools. | 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.