Ncbi Variation Tools

Configuration File: ncbi_variation_tools.json Tool Type: Local Tools Count: 8

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

Available Tools

NCBIVariation_alfa_frequencies_by_rsid (Type: NCBIVariationTool)

Get ALFA (Allele Frequency Aggregator) per-ancestry allele frequencies for a dbSNP rsID from NCBI…

NCBIVariation_alfa_frequencies_by_rsid tool specification

Tool Information:

• Name: NCBIVariation_alfa_frequencies_by_rsid

• Type: NCBIVariationTool

• Description: Get ALFA (Allele Frequency Aggregator) per-ancestry allele frequencies for a dbSNP rsID from NCBI Variation Services. Unlike dbSNP esummary global_mafs (one aggregate global frequency per study), this returns allele COUNTS and computed frequencies broken down by population/ancestry: European, African, African American, East Asian, Latin American, South Asian, Other Asian, etc. SAMN biosample IDs are resolved to ancestry names via the live ALFA frequency metadata, aggregating >1M dbGaP subjects. Accepts rsID with or without ‘rs’ prefix.

Parameters:

• rsid (string) (required) dbSNP reference SNP ID. Examples: ‘rs429358’ (APOE, per-ancestry C allele frequency), ‘rs334’ (sickle-cell HBB, per-ancestry A/T counts), ‘rs7412’ (APOE epsilon-2)

Example Usage:

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

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)

NCBIVariation_spdi_to_rsids (Type: NCBIVariationTool)

Reverse lookup from a normalized SPDI variant to the co-located dbSNP rsID(s), using NCBI Variati…

NCBIVariation_spdi_to_rsids tool specification

Tool Information:

• Name: NCBIVariation_spdi_to_rsids

• Type: NCBIVariationTool

• Description: Reverse lookup from a normalized SPDI variant to the co-located dbSNP rsID(s), using NCBI Variation Services /spdi/{spdi}/rsids. Complements the forward direction (rsid_lookup) and the SPDI conversion tools, letting you recover an rsID from a genomic SPDI/coordinate. SPDI format: ‘SeqID:Position:DeletedSequence:InsertedSequence’ (0-based interbase). Returns a list of integer rsIDs.

Parameters:

• spdi (string) (required) Variant in SPDI notation (SeqID:Position:Deleted:Inserted). Examples: ‘NC_000019.10:44908683:T:C’ (recovers rs429358 APOE), ‘NC_000001.11:230710047:A:G’ (AGT)

Example Usage:

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

NCBIVariation_vcf_to_spdi (Type: NCBIVariationTool)

Convert a raw VCF four-field variant (chromosome RefSeq accession, position, reference allele, al…

NCBIVariation_vcf_to_spdi tool specification

Tool Information:

• Name: NCBIVariation_vcf_to_spdi

• Type: NCBIVariationTool

• Description: Convert a raw VCF four-field variant (chromosome RefSeq accession, position, reference allele, alternate allele) directly to a normalized contextual SPDI on a RefSeq sequence, using NCBI Variation Services /vcf/{chrom}/{pos}/{ref}/{alts}/contextuals. Lets you enter the SPDI pipeline from VCF coordinates without first building an HGVS string. Position is 1-based VCF coordinate; the returned SPDI position is 0-based interbase.

Parameters:

• chrom (string) (required) Chromosome RefSeq accession (e.g., ‘NC_000007.14’ for chr7 GRCh38, ‘NC_000019.10’ for chr19)

• pos (string) (required) 1-based VCF position (e.g., ‘140753336’ for BRAF V600E, ‘44908684’ for APOE rs429358)

• ref (string) (required) Reference allele (e.g., ‘A’, ‘T’, ‘G’, ‘C’)

• alt (string) (required) Alternate allele (e.g., ‘T’, ‘C’). Single allele; comma-separated alts also accepted by the API.

Example Usage:

query = {
    "name": "NCBIVariation_vcf_to_spdi",
    "arguments": {
        "chrom": "example_value",
        "pos": "example_value",
        "ref": "example_value",
        "alt": "example_value"
    }
}
result = tu.run(query)

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