Ldsc Tools

Configuration File: remote_tools/ldsc_tools.json Tool Type: Remote Tools Count: 2

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

Available Tools

run_ldsc_genetic_correlation (Type: RemoteTool)

Estimate the genetic correlation (rg) between two traits from their GWAS summary statistics with …

run_ldsc_genetic_correlation tool specification

Tool Information:

  • Name: run_ldsc_genetic_correlation

  • Type: RemoteTool

  • Description: Estimate the genetic correlation (rg) between two traits from their GWAS summary statistics with cross-trait LD Score regression (Bulik-Sullivan 2015), using the Python-3 engine (NCI CBIIT/ldsc). Input two munged .sumstats(.gz) files; returns rg with SE and p-value. Requires multi-GB LD-score reference panels staged on the server; hosted alternative: https://ldlink.nih.gov/ldscore.

Parameters:

  • sumstats_path_1 (string) (required) Munged .sumstats.gz for trait 1.

  • sumstats_path_2 (string) (required) Munged .sumstats.gz for trait 2.

  • ref_ld_chr (string) (optional) Reference LD-score prefix/dir (default ‘eur_w_ld_chr/’).

  • w_ld_chr (string) (optional) Regression-weight LD-score prefix/dir (default same as ref_ld_chr).

Example Usage:

query = {
    "name": "run_ldsc_genetic_correlation",
    "arguments": {
        "sumstats_path_1": "example_value",
        "sumstats_path_2": "example_value"
    }
}
result = tu.run(query)

run_ldsc_heritability (Type: RemoteTool)

Estimate SNP-heritability from GWAS summary statistics with LD Score regression (Bulik-Sullivan 2…

run_ldsc_heritability tool specification

Tool Information:

  • Name: run_ldsc_heritability

  • Type: RemoteTool

  • Description: Estimate SNP-heritability from GWAS summary statistics with LD Score regression (Bulik-Sullivan 2015), using the maintained Python-3 engine (NCI CBIIT/ldsc). Input a munged .sumstats(.gz) file; returns observed-scale h2 with SE, the LD-score-regression intercept (confounding/inflation diagnostic), and the ratio. Requires multi-GB LD-score reference panels staged on the server; hosted alternative: https://ldlink.nih.gov/ldscore.

Parameters:

  • sumstats_path (string) (required) Server-accessible path to a munged .sumstats.gz file (output of munge_sumstats.py).

  • ref_ld_chr (string) (optional) Reference LD-score prefix/dir (default ‘eur_w_ld_chr/’, resolved under LDSC_REF_DIR).

  • w_ld_chr (string) (optional) Regression-weight LD-score prefix/dir (default same as ref_ld_chr).

Example Usage:

query = {
    "name": "run_ldsc_heritability",
    "arguments": {
        "sumstats_path": "example_value"
    }
}
result = tu.run(query)