Ldlink Tools¶
Configuration File: ldlink_tools.json
Tool Type: Local
Tools Count: 1
This page contains all tools defined in the ldlink_tools.json configuration file.
Available Tools¶
LDlink_get_proxies (Type: LDlinkTool)¶
Find variants in linkage disequilibrium (LD proxies) with a query SNP, population-specific, via N…
LDlink_get_proxies tool specification
Tool Information:
Name:
LDlink_get_proxiesType:
LDlinkToolDescription: Find variants in linkage disequilibrium (LD proxies) with a query SNP, population-specific, via NIH LDlink’s LDproxy module. Essential for GWAS interpretation: a lead SNP is often just a tag for the true causal variant, so high-R2 proxies (especially in coding/regulatory regions) are better mechanistic candidates. Returns proxy rsIDs with R2, coordinates, alleles, MAF, and distance. Requires a free LDlink token (LDLINK_TOKEN env var; register at ldlink.nih.gov).
Parameters:
variant(string) (required) Query SNP rsID, e.g. ‘rs7903146’.population([‘string’, ‘null’]) (optional) 1000 Genomes population code (default ‘CEU’). Examples: ‘CEU’ (European), ‘YRI’ (African), ‘CHB’ (East Asian), or super-populations ‘EUR’/’AFR’/’EAS’/’SAS’/’AMR’.r2_threshold([‘number’, ‘null’]) (optional) Minimum R2 to report (default 0.8; high LD).genome_build([‘string’, ‘null’]) (optional) ‘grch38’ (default) or ‘grch37’.limit([‘integer’, ‘null’]) (optional) Max proxies to return (1-500, default 50).
Example Usage:
query = {
"name": "LDlink_get_proxies",
"arguments": {
"variant": "example_value"
}
}
result = tu.run(query)