Colocalization Tools

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

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

Available Tools

Coloc_abf_test (Type: ColocalizationTool)

Bayesian colocalization (coloc.abf, Giambartolomei 2014) of two GWAS/QTL signals over the same SN…

Coloc_abf_test tool specification

Tool Information:

  • Name: Coloc_abf_test

  • Type: ColocalizationTool

  • Description: Bayesian colocalization (coloc.abf, Giambartolomei 2014) of two GWAS/QTL signals over the same SNP set in a region. Tests whether the two traits share a single causal variant. Returns the five posterior probabilities PP0-PP4; PP4 (>0.8 = strong) is the probability of a shared causal variant - the standard way to link a GWAS locus to a gene via an eQTL. Pure-compute (no R, no LD matrix); pairs with eQTL_get_associations + GWAS summary tools.

Parameters:

  • beta1 (array) (required) Trait 1 per-SNP effect sizes over the region (same SNP order as trait 2).

  • se1 (array) (required) Standard errors of beta1 (positive).

  • beta2 (array) (required) Trait 2 per-SNP effect sizes (same SNP order/alleles).

  • se2 (array) (required) Standard errors of beta2 (positive).

  • snp ([‘array’, ‘null’]) (optional) Optional SNP identifiers (same order) to label the best shared variant.

  • sd_prior ([‘number’, ‘null’]) (optional) Prior SD of the effect size (default 0.15; 0.2 common for case/control log-OR).

  • p1 ([‘number’, ‘null’]) (optional) Prior prob a SNP is causal for trait 1 (default 1e-4).

  • p2 ([‘number’, ‘null’]) (optional) Prior prob a SNP is causal for trait 2 (default 1e-4).

  • p12 ([‘number’, ‘null’]) (optional) Prior prob a SNP is causal for both traits (default 1e-5).

Example Usage:

query = {
    "name": "Coloc_abf_test",
    "arguments": {
        "beta1": ["item1", "item2"],
        "se1": ["item1", "item2"],
        "beta2": ["item1", "item2"],
        "se2": ["item1", "item2"]
    }
}
result = tu.run(query)