Fine-Mapping Tool Requirements

Use this page when you are deciding whether a prepared locus has enough data for a specific fine-mapping tool.

Short Version

Tool	Input mode	LD needed by method	Extra software	Notes
abf	single input	no	none	ABF assumes one causal signal; CLI still expects LD files when loading from loci_list.txt.
abf_cojo	single input	yes	none	Uses COJO-style conditioning before ABF.
susie	single input	yes	none	Good default for most first-pass runs.
susie_ash	single input	yes	Rscript, susieR >= 0.16.1	SuSiE with adaptive-shrinkage background.
susie_inf	single input	yes	Rscript, susieR >= 0.16.1	SuSiE with infinitesimal background.
finemap	single input	yes	finemap executable	Requires MAF; has a per-locus timeout.
rsparsepro	single input	yes	none	Robust sparse model for LD mismatch sensitivity checks.
carma	single input	yes	Rscript, CARMA	Includes CARMA outlier modeling.
multisusie	multi input	yes	none	Joint multi-population SuSiE-style model.
susiex	multi input	yes	SuSiEx executable	Cross-ancestry fine-mapping wrapper.
mesusie	multi input	yes	Rscript, MESuSiE	Joint multi-ancestry model with shared and ancestry-specific signals.

Single input versus multi input

Single-input tools run once per row in a locus set and CREDTOOLS combines the results. Multi-input tools analyze all rows for the same locus_id together.

Required Columns

All CLI fine-mapping workflows start from loci_list.txt:

locus_id    chr start   end popu    cohort  sample_size prefix

Each prefix should resolve to:

{prefix}.sumstats.gz
{prefix}.ld.npz
{prefix}.ldmap.gz

The summary statistics should contain:

Column	Used for
SNPID	matching summary statistics to LD
CHR, BP	location and plotting
EA, NEA	allele alignment
EAF	allele-frequency checks and derived MAF
MAF	required by FINEMAP; usually derived from EAF when loaded
BETA, SE, P	all fine-mapping models
N	useful in prepared files; CLI also uses sample_size from loci_list.txt
RSID	optional reporting field

No-Signal Behavior

Most single-input wrappers check --significant-threshold before running the model. If no variant passes the threshold, CREDTOOLS returns an empty result instead of forcing a weak credible set.

credtools finemap loci_list.txt results \
  --tool susie \
  --significant-threshold 5e-8

An empty result usually has:

• n_cs = 0
• PIP = 0 for every variant
• no rows in causal_variants.txt.gz

If that is not what you want, loosen --significant-threshold for exploratory runs and label the output accordingly.

Convergence Options

Iterative tools expose --max-iter and convergence tolerance options. When using adaptive search:

credtools pipeline loci_list.txt results \
  --tool susie \
  --adaptive-max-causal

CREDTOOLS starts from the requested --max-causal, tries larger values if the model appears capped, and can retry smaller values when convergence fails.

For SuSiEx, keep --mult-step off when using --adaptive-max-causal; both features try to refine the model and can make debugging harder.

Choosing the First Tool

Start with:

credtools pipeline loci_list.txt results \
  --tool susie \
  --meta-method meta_all \
  --max-causal 5

Then compare a smaller set of important loci with another tool:

credtools finemap important_loci.txt results_finemap \
  --tool finemap \
  --max-causal 5 \
  --timeout-minutes 30

Use comparison runs to answer a specific question, such as whether a top credible set is stable under a different model.