Dbsnp Tools#

Configuration File: dbsnp_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

dbsnp_get_frequencies (Type: dbSNPGetFrequencies)#

Get allele frequencies for a variant from dbSNP. Returns population-specific allele frequency dat…

dbsnp_get_frequencies tool specification

Tool Information:

  • Name: dbsnp_get_frequencies

  • Type: dbSNPGetFrequencies

  • Description: Get allele frequencies for a variant from dbSNP. Returns population-specific allele frequency data. Each study reports an ‘allele_count’ – the number of ALLELES (chromosomes) observed carrying the allele, NOT a number of individuals. Do not read it as study size: for a diploid cohort the number of people is at most half of it, and the denominator is the cohort’s total allele count, which dbSNP does not report here.

Parameters:

  • rsid (string) (required) dbSNP rsID (e.g., ‘rs12345’, ‘12345’)

Example Usage:

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

dbsnp_get_variant_by_rsid (Type: dbSNPGetVariantByRsID)#

Get variant information from dbSNP by rsID. Returns genomic coordinates, alleles, and basic varia…

dbsnp_get_variant_by_rsid tool specification

Tool Information:

  • Name: dbsnp_get_variant_by_rsid

  • Type: dbSNPGetVariantByRsID

  • Description: Get variant information from dbSNP by rsID. Returns genomic coordinates, alleles, and basic variant information. Coordinates are reported on BOTH assemblies: ‘position’/’position_grch38’ are on GRCh38 (dbSNP’s current assembly, named by the ‘assembly’ field) and ‘position_grch37’ is the same variant on GRCh37. Always pick the field matching your pipeline’s build – the two can differ by hundreds of kilobases.

Parameters:

  • rsid (string) (required) dbSNP rsID (e.g., ‘rs12345’, ‘12345’)

Example Usage:

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

dbsnp_search_by_gene (Type: dbSNPSearchByGene)#

Search dbSNP variants by gene symbol with complete offset pagination. The response reports dbSNP’…

dbsnp_search_by_gene tool specification

Tool Information:

  • Name: dbsnp_search_by_gene

  • Type: dbSNPSearchByGene

  • Description: Search dbSNP variants by gene symbol with complete offset pagination. The response reports dbSNP’s exact total_count plus returned_count, has_more, and next_offset; continue with offset=next_offset until has_more is false instead of treating the first page as the full variant set.

Parameters:

  • gene_symbol (string) (required) Gene symbol (e.g., ‘BRCA1’, ‘TP53’, ‘APOE’)

  • limit (integer) (optional) Number of variants requested for this page (1-100).

  • offset (integer) (optional) Zero-based result offset, mapped to NCBI ESearch retstart. Use data.next_offset to fetch the following page.

Example Usage:

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