Finemap Abf Tools

Configuration File: finemap_abf_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the finemap_abf_tools.json configuration file.

Available Tools

Finemap_credible_set (Type: FinemapABFTool)

Single-causal-variant fine-mapping from GWAS/QTL summary statistics (per-SNP effect size + SE ove…

Finemap_credible_set tool specification

Tool Information:

  • Name: Finemap_credible_set

  • Type: FinemapABFTool

  • Description: Single-causal-variant fine-mapping from GWAS/QTL summary statistics (per-SNP effect size + SE over a region). Computes each SNP’s posterior inclusion probability (PIP) via Wakefield approximate Bayes factors and the 95% credible set (smallest SNP set capturing the causal variant). LD-free (assumes one causal signal); pure-compute, no R. For multi-signal loci use SuSiE/FINEMAP with LD.

Parameters:

  • beta (array) (required) Per-SNP effect sizes over the region.

  • se (array) (required) Standard errors of beta (positive).

  • snp ([‘array’, ‘null’]) (optional) Optional SNP identifiers (same order) to label PIPs and the credible set.

  • coverage ([‘number’, ‘null’]) (optional) Credible-set coverage in (0,1] (default 0.95).

  • sd_prior ([‘number’, ‘null’]) (optional) Prior SD of the effect size (default 0.15).

Example Usage:

query = {
    "name": "Finemap_credible_set",
    "arguments": {
        "beta": ["item1", "item2"],
        "se": ["item1", "item2"]
    }
}
result = tu.run(query)