credtools pipeline

Run meta-analysis, QC, and fine-mapping in one command.

credtools pipeline INPUTS OUTDIR [OPTIONS]

Common Use

credtools pipeline work/chunks/loci_list.txt work/results \
  --tool susie \
  --meta-method meta_all

Workflow

For each locus_id, the pipeline:

1. loads all rows for the locus,
2. computes heterogeneity,
3. runs the selected meta-analysis method,
4. runs QC unless --skip-qc is set,
5. runs fine-mapping,
6. writes result tables and logs.

Main Options

Option	Meaning	Default
--meta-method	meta_all, meta_by_population, or no_meta	meta_all
--skip-qc	skip the QC phase	off
--tool	fine-mapping engine	susie
--max-causal	maximum causal variants	5
--adaptive-max-causal	retry with adjusted max_causal	off
--set-L-by-cojo	estimate signal count with COJO	on
--coverage	credible set coverage	0.95
--significant-threshold	p-value threshold for considering a signal	5e-8
--combine-cred	combine credible sets from separate runs	union
--combine-pip	combine PIPs from separate runs	max
--jaccard-threshold	cluster threshold for credible sets	0.1
--calculate-lambda-s	estimate lambda-s while loading loci	off
--log-file	write logs to a file	none

Selected Tool-Specific Options

Tool family	Options
ABF	--var-prior
FINEMAP	--n-iter, --n-threads
SuSiE	--max-iter, --estimate-residual-variance, --purity, --convergence-tol
RSparsePro	--eps, --ubound, --cthres, --eincre, --minldthres, --maxldthres, --varemax, --varemin
SuSiEx	--mult-step, --keep-ambig, --min-purity, --tol
CARMA	--outlier-switch, --effect-size-prior
MULTISUSIE	--rho, --scaled-prior-variance, --standardize, --pop-spec-standardization, --estimate-prior-variance, --estimate-prior-method, --pop-spec-effect-priors, --iter-before-zeroing-effects, --prior-tol

Use credtools pipeline --help for the full current flag list.

Outputs

OUTDIR/
- overall_run_summary.log
- {locus_id}/
  - pips.txt.gz
  - credible_sets_summary.txt.gz
  - causal_variants.txt.gz
  - parameters.json
  - run_summary.log
  - QC tables