Ncbi Variation Tools

Configuration File: ncbi_variation_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

NCBIVariation_hgvs_to_spdi (Type: NCBIVariationTool)

Convert an HGVS variant description to SPDI notation using NCBI Variation Services. Accepts any v…

NCBIVariation_hgvs_to_spdi tool specification

Tool Information:

  • Name: NCBIVariation_hgvs_to_spdi

  • Type: NCBIVariationTool

  • Description: Convert an HGVS variant description to SPDI notation using NCBI Variation Services. Accepts any valid HGVS description (genomic g., coding c., or RNA r.) and returns the equivalent SPDI representation(s). Also validates the input HGVS expression. Useful for normalizing variant representations and converting between notation systems.

Parameters:

  • hgvs (string) (required) HGVS variant description. Examples: ‘NC_000001.11:g.230710048A>G’ (genomic), ‘NM_000059.4:c.68_69del’ (coding deletion in BRCA2), ‘NM_000546.6:c.215C>G’ (TP53 Pro72Arg)

Example Usage:

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

NCBIVariation_rsid_lookup (Type: NCBIVariationTool)

Look up a dbSNP rsID and retrieve variant details including GRCh38 genomic coordinates, associate…

NCBIVariation_rsid_lookup tool specification

Tool Information:

  • Name: NCBIVariation_rsid_lookup

  • Type: NCBIVariationTool

  • Description: Look up a dbSNP rsID and retrieve variant details including GRCh38 genomic coordinates, associated genes, clinical significance (ClinVar), citations, and MANE Select transcript IDs. Accepts rsID with or without ‘rs’ prefix (e.g., ‘rs429358’ or ‘429358’). Returns structured summary of the variant.

Parameters:

  • rsid (string) (required) dbSNP reference SNP ID. Examples: ‘rs429358’ (APOE epsilon-4 allele), ‘rs7412’ (APOE epsilon-2), ‘rs699’ (AGT M235T), ‘rs1801133’ (MTHFR C677T)

Example Usage:

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

NCBIVariation_spdi_canonical (Type: NCBIVariationTool)

Get the canonical (normalized) SPDI representation for a variant. Returns the single canonical fo…

NCBIVariation_spdi_canonical tool specification

Tool Information:

  • Name: NCBIVariation_spdi_canonical

  • Type: NCBIVariationTool

  • Description: Get the canonical (normalized) SPDI representation for a variant. Returns the single canonical form of a variant after normalization (right-shifting for indels, using the top-level chromosome sequence). Useful for variant deduplication and consistent storage.

Parameters:

  • spdi (string) (required) Variant in SPDI notation to normalize. Examples: ‘NC_000001.11:230710047:A:G’, ‘NM_000546.6:214:C:G’ (TP53)

Example Usage:

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

NCBIVariation_spdi_equivalents (Type: NCBIVariationTool)

Get all equivalent SPDI representations of a variant across different reference sequences and gen…

NCBIVariation_spdi_equivalents tool specification

Tool Information:

  • Name: NCBIVariation_spdi_equivalents

  • Type: NCBIVariationTool

  • Description: Get all equivalent SPDI representations of a variant across different reference sequences and genome assemblies (GRCh37/GRCh38, RefSeqGene, transcript). Given one SPDI, returns the same variant mapped to all available coordinate systems. Useful for liftover between assemblies and cross-referencing variants described on different reference sequences.

Parameters:

  • spdi (string) (required) Variant in SPDI notation. Examples: ‘NC_000001.11:230710047:A:G’ (GRCh38 AGT variant), ‘NM_000059.4:266:AT:’ (BRCA2 transcript-level)

Example Usage:

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

NCBIVariation_spdi_to_hgvs (Type: NCBIVariationTool)

Convert a variant in SPDI notation to HGVS notation using NCBI Variation Services. SPDI (Sequence…

NCBIVariation_spdi_to_hgvs tool specification

Tool Information:

  • Name: NCBIVariation_spdi_to_hgvs

  • Type: NCBIVariationTool

  • Description: Convert a variant in SPDI notation to HGVS notation using NCBI Variation Services. SPDI (Sequence Position Deletion Insertion) is NCBI’s canonical variant representation. Input format: ‘SeqID:Position:DeletedSequence:InsertedSequence’ (e.g., ‘NC_000001.11:230710047:A:G’). Returns the equivalent HGVS genomic description (e.g., ‘NC_000001.11:g.230710048A>G’). Note: SPDI uses 0-based interbase coordinates, while HGVS uses 1-based.

Parameters:

  • spdi (string) (required) Variant in SPDI notation (SeqID:Position:Deleted:Inserted). Examples: ‘NC_000001.11:230710047:A:G’ (AGT M259T), ‘NC_000017.11:7674220:G:C’ (TP53 region), ‘NM_000059.4:266:AT:’ (BRCA2 c.68_69del)

Example Usage:

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