credtools finemap

Run fine-mapping without the full pipeline.

credtools finemap INPUTS OUTDIR [OPTIONS]

Common Use

credtools finemap work/chunks/loci_list.txt work/finemap \
  --tool susie \
  --max-causal 5

Tool Choice

Tool	Type
abf	single-input
abf_cojo	single-input
carma	single-input
finemap	single-input
rsparsepro	single-input
susie	single-input
susie_ash	single-input
susie_inf	single-input
multisusie	multi-input
susiex	multi-input
mesusie	multi-input

Common Options

Option	Meaning	Default
--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	off
--coverage	credible set coverage	0.95
--timeout-minutes	per-locus FINEMAP timeout	30 for FINEMAP
--processes	per-locus worker processes	1
--combine-cred	union, intersection, or cluster	union
--combine-pip	max, min, mean, or meta	max
--significant-threshold	p-value threshold for considering a signal	5e-8
--jaccard-threshold	clustering threshold for credible sets	0.1
--purity	minimum credible set purity	0.0
--calculate-lambda-s	estimate lambda-s while loading loci	off
--log-file	write logs to a file	none

For exact adaptive-L retry rules, see Adaptive L.

SuSiE Options

Option	Default
--max-iter	100
--estimate-residual-variance	off
--convergence-tol	1e-3

--convergence-tol also controls the outer stopping tolerance for MultiSuSiE and MESuSiE. MESuSiE defaults to covariance EM; use --mesusie-optimizer native to select the original covariance optimizer. Both modes use guarded outer convergence. See the R/compiler requirements.

COJO Options

Used with --set-L-by-cojo.

Option	Default
--p-cutoff	5e-8
--collinear-cutoff	0.9
--window-size	10000000
--maf-cutoff	0.01
--diff-freq-cutoff	0.2

Outputs

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