GeneBe
Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only.
Should I use this
Quality & Safety
A
Based on automated analysis of tool definitions and protocol compliance.
Context Cost
~5,264Tokens (tool definitions)
~8.9 KBTypical response size
Significant attention impact (4.11% of 128k context)
This is the approximate number of tokens consumed each time the server's tools are loaded into a model's context. Higher counts reduce the attention available for other tasks.
Install
One-Click Install
Add this to your `claude_desktop_config.json` file:
{
"mcpServers": {
"genebe-mcp": {
"url": "https://mcp.genebe.net/v1/mcp"
}
}
}Remote endpoints
https://mcp.genebe.net/v1/mcpstreamable-httpWhat it can do
Tool inventory
Tools (6)
🟢 Read-only🟡 Write🔴 Delete⚪ Unknown
🟢annotate_variant(variant, genome, transcript, gene_symbol)
Annotate and classify one human genetic variant using GeneBe. Start here for any question about a variant (what is it, is it pathogenic/benign, how common is it). Returns the ACMG verdict with points and criteria, population frequency (gnomAD), predictor scores (REVEL, AlphaMissense, SpliceAI, ...), ClinVar status, transcript consequences, and links to the GeneBe page to cite. Research use only; not a diagnosis.
Input Schema
{
"type": "object",
"properties": {
"variant": {
"description": "The variant. Accepts 'chr-pos-ref-alt' (6-160585140-T-G), HGVS with transcript (NM_005577.4:c.4195A>C), rsID (rs41272110), SPDI, or 'GENE p.Thr1399Pro'.",
"title": "Variant",
"type": "string"
},
"genome": {
"default": "hg38",
"description": "Genome build of coordinate input. Ignored for HGVS/rsID.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "Genome",
"type": "string"
},
"transcript": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Force this transcript for the classification, e.g. NM_000546.6",
"title": "Transcript"
},
"gene_symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Force this gene for the classification, e.g. TP53",
"title": "Gene Symbol"
}
},
"required": [
"variant"
],
"title": "annotate_variantArguments"
}Output Schema
{
"type": "object",
"properties": {
"summary": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable variant summary from GeneBe, when the backend provides one",
"title": "Summary"
},
"variant": {
"$ref": "#/$defs/VariantCoordinates"
},
"dbsnp": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Dbsnp"
},
"verdict": {
"$ref": "#/$defs/Verdict"
},
"frequency": {
"$ref": "#/$defs/Frequency"
},
"consequences": {
"items": {
"$ref": "#/$defs/Consequence"
},
"title": "Consequences",
"type": "array"
},
"total_consequences": {
"title": "Total Consequences",
"type": "integer"
},
"scores": {
"$ref": "#/$defs/Scores"
},
"clinvar": {
"anyOf": [
{
"$ref": "#/$defs/ClinVar"
},
{
"type": "null"
}
]
},
"conservation": {
"additionalProperties": {
"$ref": "#/$defs/Score"
},
"title": "Conservation",
"type": "object"
},
"gene": {
"$ref": "#/$defs/GeneRef"
},
"links": {
"$ref": "#/$defs/Links"
},
"warning": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Warning"
},
"truncated": {
"default": false,
"title": "Truncated",
"type": "boolean"
},
"disclaimer": {
"default": "For research use only. Not a diagnosis; results must be reviewed by a qualified specialist before any clinical use.",
"title": "Disclaimer",
"type": "string"
}
},
"required": [
"variant",
"dbsnp",
"verdict",
"frequency",
"consequences",
"total_consequences",
"scores",
"clinvar",
"conservation",
"gene",
"links"
],
"$defs": {
"ClinVar": {
"properties": {
"classification": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Classification"
},
"review_status": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Review Status"
},
"conditions": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Conditions"
}
},
"required": [
"classification",
"review_status",
"conditions"
],
"title": "ClinVar",
"type": "object"
},
"Consequence": {
"properties": {
"transcript": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Transcript"
},
"gene_symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene Symbol"
},
"consequences": {
"items": {
"type": "string"
},
"title": "Consequences",
"type": "array"
},
"hgvs_c": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs C"
},
"hgvs_p": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs P"
},
"mane_select": {
"title": "Mane Select",
"type": "boolean"
},
"canonical": {
"title": "Canonical",
"type": "boolean"
},
"exon_rank": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Exon Rank"
},
"exon_count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Exon Count"
}
},
"required": [
"transcript",
"gene_symbol",
"consequences",
"hgvs_c",
"hgvs_p",
"mane_select",
"canonical",
"exon_rank",
"exon_count"
],
"title": "Consequence",
"type": "object"
},
"Criterion": {
"properties": {
"code": {
"description": "Criterion with strength, e.g. 'BA1' or 'PP3_Strong'",
"title": "Code",
"type": "string"
},
"reason": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Why the criterion fired, when the backend provides it",
"title": "Reason"
}
},
"required": [
"code"
],
"title": "Criterion",
"type": "object"
},
"Frequency": {
"properties": {
"combined": {
"$ref": "#/$defs/PopulationCounts"
},
"gnomad_exomes": {
"$ref": "#/$defs/PopulationCounts"
},
"gnomad_genomes": {
"$ref": "#/$defs/PopulationCounts"
}
},
"required": [
"combined",
"gnomad_exomes",
"gnomad_genomes"
],
"title": "Frequency",
"type": "object"
},
"GeneRef": {
"properties": {
"symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Symbol"
},
"hgnc_id": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Hgnc Id"
},
"transcript": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"description": "Transcript used for the classification",
"title": "Transcript"
}
},
"required": [
"symbol",
"hgnc_id",
"transcript"
],
"title": "GeneRef",
"type": "object"
},
"GeneVerdict": {
"properties": {
"gene_symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene Symbol"
},
"transcript": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Transcript"
},
"hgvs_c": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs C"
},
"hgvs_p": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs P"
},
"classification": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Classification"
},
"points": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Points"
},
"criteria": {
"items": {
"type": "string"
},
"title": "Criteria",
"type": "array"
}
},
"required": [
"gene_symbol",
"transcript",
"hgvs_c",
"hgvs_p",
"classification",
"points",
"criteria"
],
"title": "GeneVerdict",
"type": "object"
},
"Links": {
"properties": {
"variant": {
"title": "Variant",
"type": "string"
},
"gene": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene"
}
},
"required": [
"variant",
"gene"
],
"title": "Links",
"type": "object"
},
"PopulationCounts": {
"properties": {
"allele_count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Allele Count"
},
"allele_frequency": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Allele Frequency"
},
"homozygotes": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Homozygotes"
}
},
"required": [
"allele_count",
"allele_frequency",
"homozygotes"
],
"title": "PopulationCounts",
"type": "object"
},
"Score": {
"properties": {
"score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Score"
},
"prediction": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Prediction"
}
},
"required": [
"score",
"prediction"
],
"title": "Score",
"type": "object"
},
"Scores": {
"properties": {
"selected_computational": {
"anyOf": [
{
"$ref": "#/$defs/Score"
},
{
"type": "null"
}
],
"description": "Predictor GeneBe picked for the ACMG call"
},
"selected_computational_source": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Selected Computational Source"
},
"selected_splice": {
"anyOf": [
{
"$ref": "#/$defs/Score"
},
{
"type": "null"
}
]
},
"selected_splice_source": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Selected Splice Source"
},
"predictors": {
"additionalProperties": {
"$ref": "#/$defs/Score"
},
"description": "Every available predictor, keyed by name",
"title": "Predictors",
"type": "object"
}
},
"required": [
"selected_computational",
"selected_computational_source",
"selected_splice",
"selected_splice_source",
"predictors"
],
"title": "Scores",
"type": "object"
},
"VariantCoordinates": {
"properties": {
"genome": {
"title": "Genome",
"type": "string"
},
"chr": {
"title": "Chr",
"type": "string"
},
"pos": {
"description": "1-based VCF position",
"title": "Pos",
"type": "integer"
},
"ref": {
"title": "Ref",
"type": "string"
},
"alt": {
"title": "Alt",
"type": "string"
}
},
"required": [
"genome",
"chr",
"pos",
"ref",
"alt"
],
"title": "VariantCoordinates",
"type": "object"
},
"Verdict": {
"properties": {
"classification": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"description": "e.g. Pathogenic, Likely_benign, Uncertain_significance",
"title": "Classification"
},
"points": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"description": "Total ACMG points; positive favours pathogenic, negative benign",
"title": "Points"
},
"criteria": {
"items": {
"$ref": "#/$defs/Criterion"
},
"title": "Criteria",
"type": "array"
},
"guideline": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Guideline"
},
"per_gene": {
"description": "Verdict for every overlapping gene, when more than one",
"items": {
"$ref": "#/$defs/GeneVerdict"
},
"title": "Per Gene",
"type": "array"
},
"disclaimer": {
"default": "For research use only. Not a diagnosis; results must be reviewed by a qualified specialist before any clinical use.",
"title": "Disclaimer",
"type": "string"
}
},
"required": [
"classification",
"points",
"criteria",
"per_gene"
],
"title": "Verdict",
"type": "object"
}
},
"title": "AnnotationResult"
}🟢explain_acmg_decision_path(variant, genome, tree, version)
Explain step by step why each classification criterion did or did not apply to a variant. Use after annotate_variant when the user asks "why was this classified that way?". Returns an ASCII rendering of the decision tree with the evaluated conditions. By default it explains the germline ACMG verdict that annotate_variant returns; the somatic trees 'oncogenicity' (2022) and 'acgs-uk-onco' (2025) can be requested explicitly. Research use only.
Input Schema
{
"type": "object",
"properties": {
"variant": {
"description": "The variant, in any notation accepted by annotate_variant.",
"title": "Variant",
"type": "string"
},
"genome": {
"default": "hg38",
"description": "Genome build of coordinate input.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "Genome",
"type": "string"
},
"tree": {
"default": "germline",
"description": "Decision tree: 'germline' (default), 'oncogenicity' or 'acgs-uk-onco'.",
"title": "Tree",
"type": "string"
},
"version": {
"default": "2019",
"description": "Tree version: germline 2019 (default), oncogenicity 2022, acgs-uk-onco 2025.",
"title": "Version",
"type": "string"
}
},
"required": [
"variant"
],
"title": "explain_acmg_decision_pathArguments"
}Output Schema
{
"type": "object",
"properties": {
"variant": {
"$ref": "#/$defs/VariantCoordinates"
},
"tree": {
"title": "Tree",
"type": "string"
},
"version": {
"title": "Version",
"type": "string"
},
"text": {
"description": "ASCII rendering of how each criterion was evaluated",
"title": "Text",
"type": "string"
},
"truncated": {
"default": false,
"title": "Truncated",
"type": "boolean"
},
"disclaimer": {
"default": "For research use only. Not a diagnosis; results must be reviewed by a qualified specialist before any clinical use.",
"title": "Disclaimer",
"type": "string"
}
},
"required": [
"variant",
"tree",
"version",
"text"
],
"$defs": {
"VariantCoordinates": {
"properties": {
"genome": {
"title": "Genome",
"type": "string"
},
"chr": {
"title": "Chr",
"type": "string"
},
"pos": {
"description": "1-based VCF position",
"title": "Pos",
"type": "integer"
},
"ref": {
"title": "Ref",
"type": "string"
},
"alt": {
"title": "Alt",
"type": "string"
}
},
"required": [
"genome",
"chr",
"pos",
"ref",
"alt"
],
"title": "VariantCoordinates",
"type": "object"
}
},
"title": "DecisionPath"
}🟢convert_variant(variant, input_genome)
Convert a variant written in any notation into normalized hg38 genomic coordinates. Use when you only need the chr/pos/ref/alt of a variant (for example to translate HGVS or an rsID), without annotation. Does not classify the variant; use annotate_variant for that.
Input Schema
{
"type": "object",
"properties": {
"variant": {
"description": "HGVS (NM_007294.4:c.3756_3759del), rsID (rs429358), SPDI (NC_000007.14:11324573:C:T), 'chr-pos-ref-alt', or 'GENE p.Thr1700Ile'.",
"title": "Variant",
"type": "string"
},
"input_genome": {
"default": "hg38",
"description": "Genome build of positional input (hg19 input is lifted to hg38).",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "Input Genome",
"type": "string"
}
},
"required": [
"variant"
],
"title": "convert_variantArguments"
}Output Schema
{
"type": "object",
"properties": {
"input": {
"title": "Input",
"type": "string"
},
"variants": {
"description": "Resolved hg38 coordinates (usually exactly one)",
"items": {
"$ref": "#/$defs/VariantCoordinates"
},
"title": "Variants",
"type": "array"
},
"error": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Error"
}
},
"required": [
"input",
"variants"
],
"$defs": {
"VariantCoordinates": {
"properties": {
"genome": {
"title": "Genome",
"type": "string"
},
"chr": {
"title": "Chr",
"type": "string"
},
"pos": {
"description": "1-based VCF position",
"title": "Pos",
"type": "integer"
},
"ref": {
"title": "Ref",
"type": "string"
},
"alt": {
"title": "Alt",
"type": "string"
}
},
"required": [
"genome",
"chr",
"pos",
"ref",
"alt"
],
"title": "VariantCoordinates",
"type": "object"
}
},
"title": "ConvertResult"
}🟢get_variant_effects(variant, genome)
List a variant's predicted molecular consequences on every overlapping transcript. Returns per-transcript HGVS (c. and p.), consequence terms (e.g. missense_variant) and impact, most severe and MANE Select transcripts first. Lightweight: no frequencies or classification.
Input Schema
{
"type": "object",
"properties": {
"variant": {
"description": "The variant, in any notation accepted by annotate_variant.",
"title": "Variant",
"type": "string"
},
"genome": {
"default": "hg38",
"description": "Genome build of coordinate input.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "Genome",
"type": "string"
}
},
"required": [
"variant"
],
"title": "get_variant_effectsArguments"
}Output Schema
{
"type": "object",
"properties": {
"variant": {
"$ref": "#/$defs/VariantCoordinates"
},
"effects": {
"items": {
"$ref": "#/$defs/Effect"
},
"title": "Effects",
"type": "array"
},
"total_effects": {
"title": "Total Effects",
"type": "integer"
},
"truncated": {
"default": false,
"title": "Truncated",
"type": "boolean"
}
},
"required": [
"variant",
"effects",
"total_effects"
],
"$defs": {
"Effect": {
"properties": {
"transcript": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Transcript"
},
"source": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Source"
},
"gene_symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene Symbol"
},
"impact": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Impact"
},
"effects": {
"items": {
"type": "string"
},
"title": "Effects",
"type": "array"
},
"hgvs_c": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs C"
},
"hgvs_p": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs P"
},
"mane_select": {
"title": "Mane Select",
"type": "boolean"
},
"canonical": {
"title": "Canonical",
"type": "boolean"
},
"exon_rank": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Exon Rank"
},
"protein_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Protein Id"
}
},
"required": [
"transcript",
"source",
"gene_symbol",
"impact",
"effects",
"hgvs_c",
"hgvs_p",
"mane_select",
"canonical",
"exon_rank",
"protein_id"
],
"title": "Effect",
"type": "object"
},
"VariantCoordinates": {
"properties": {
"genome": {
"title": "Genome",
"type": "string"
},
"chr": {
"title": "Chr",
"type": "string"
},
"pos": {
"description": "1-based VCF position",
"title": "Pos",
"type": "integer"
},
"ref": {
"title": "Ref",
"type": "string"
},
"alt": {
"title": "Alt",
"type": "string"
}
},
"required": [
"genome",
"chr",
"pos",
"ref",
"alt"
],
"title": "VariantCoordinates",
"type": "object"
}
},
"title": "EffectsResult"
}🟢get_gene(gene, include_transcripts)
Look up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity. Use for questions about a gene rather than a specific variant. Transcripts are listed with MANE Select first and capped; check total_transcripts.
Input Schema
{
"type": "object",
"properties": {
"gene": {
"description": "Gene symbol (BRCA1), alias, HGNC id (HGNC:1100), 'entrez:672' or Ensembl id (ENSG...).",
"title": "Gene",
"type": "string"
},
"include_transcripts": {
"default": true,
"description": "Also list the gene's transcripts.",
"title": "Include Transcripts",
"type": "boolean"
}
},
"required": [
"gene"
],
"title": "get_geneArguments"
}Output Schema
{
"type": "object",
"properties": {
"symbol": {
"title": "Symbol",
"type": "string"
},
"name": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Name"
},
"hgnc_id": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Hgnc Id"
},
"ncbi_id": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Ncbi Id"
},
"ensembl_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Ensembl Id"
},
"omim_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Omim Id"
},
"uniprot_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Uniprot Id"
},
"chr": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Chr"
},
"start": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Start"
},
"end": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "End"
},
"mane_select_refseq": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Mane Select Refseq"
},
"mane_select_ensembl": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Mane Select Ensembl"
},
"gene_disease_validity": {
"items": {
"$ref": "#/$defs/GeneDisease"
},
"title": "Gene Disease Validity",
"type": "array"
},
"total_gene_disease_entries": {
"title": "Total Gene Disease Entries",
"type": "integer"
},
"message": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Set when an alias matched several genes",
"title": "Message"
},
"alternative_hgnc_ids": {
"items": {
"type": "string"
},
"title": "Alternative Hgnc Ids",
"type": "array"
},
"transcripts": {
"items": {
"$ref": "#/$defs/TranscriptSummary"
},
"title": "Transcripts",
"type": "array"
},
"total_transcripts": {
"title": "Total Transcripts",
"type": "integer"
},
"truncated": {
"default": false,
"title": "Truncated",
"type": "boolean"
},
"link": {
"title": "Link",
"type": "string"
}
},
"required": [
"symbol",
"name",
"hgnc_id",
"ncbi_id",
"ensembl_id",
"omim_id",
"uniprot_id",
"chr",
"start",
"end",
"mane_select_refseq",
"mane_select_ensembl",
"gene_disease_validity",
"total_gene_disease_entries",
"transcripts",
"total_transcripts",
"link"
],
"$defs": {
"GeneDisease": {
"properties": {
"disease": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Disease"
},
"classification": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"description": "ClinGen gene-disease validity",
"title": "Classification"
}
},
"required": [
"disease",
"classification"
],
"title": "GeneDisease",
"type": "object"
},
"TranscriptSummary": {
"properties": {
"id": {
"title": "Id",
"type": "string"
},
"protein_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Protein Id"
},
"mane_select": {
"title": "Mane Select",
"type": "boolean"
},
"mane_plus_clinical": {
"title": "Mane Plus Clinical",
"type": "boolean"
},
"coding_exons": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Coding Exons"
}
},
"required": [
"id",
"protein_id",
"mane_select",
"mane_plus_clinical",
"coding_exons"
],
"title": "TranscriptSummary",
"type": "object"
}
},
"title": "GeneResult"
}🟢liftover_coordinate(query, from_genome, to_genome)
Convert a genomic position, interval or variant between genome builds (hg19, hg38, t2t). Check `status`: RESOLVED means one result, AMBIGUOUS means several candidates, anything else means it could not be mapped (see errors). For variants, ref/alt are rebuilt against the target reference and warnings such as REF_MISMATCH may apply.
Input Schema
{
"type": "object",
"properties": {
"query": {
"description": "A position ('chr8:141310715'), an interval ('chr8:141310715-141310716') or a variant ('chr2-23423-A-C', HGVS, rsID).",
"title": "Query",
"type": "string"
},
"from_genome": {
"description": "Genome build of the input.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "From Genome",
"type": "string"
},
"to_genome": {
"description": "Genome build to convert to.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "To Genome",
"type": "string"
}
},
"required": [
"query",
"from_genome",
"to_genome"
],
"title": "liftover_coordinateArguments"
}Output Schema
{
"type": "object",
"properties": {
"input": {
"title": "Input",
"type": "string"
},
"from_genome": {
"title": "From Genome",
"type": "string"
},
"to_genome": {
"title": "To Genome",
"type": "string"
},
"status": {
"description": "RESOLVED, AMBIGUOUS, UNRESOLVED, INVALID, NOT_RECOGNIZED or UNSUPPORTED",
"title": "Status",
"type": "string"
},
"candidates": {
"items": {
"$ref": "#/$defs/LiftoverCandidate"
},
"title": "Candidates",
"type": "array"
},
"warnings": {
"items": {
"$ref": "#/$defs/Issue"
},
"title": "Warnings",
"type": "array"
},
"errors": {
"items": {
"$ref": "#/$defs/Issue"
},
"title": "Errors",
"type": "array"
}
},
"required": [
"input",
"from_genome",
"to_genome",
"status",
"candidates",
"warnings",
"errors"
],
"$defs": {
"Issue": {
"properties": {
"code": {
"title": "Code",
"type": "string"
},
"message": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Message"
}
},
"required": [
"code",
"message"
],
"title": "Issue",
"type": "object"
},
"LiftoverCandidate": {
"properties": {
"chr": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Chr"
},
"start": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Start"
},
"end": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "End"
},
"genome": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Genome"
},
"strand": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Strand"
},
"ref": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Ref"
},
"alt": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Alt"
},
"percent_mapped": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Percent Mapped"
}
},
"required": [
"chr",
"start",
"end",
"genome",
"strand",
"percent_mapped"
],
"title": "LiftoverCandidate",
"type": "object"
}
},
"title": "LiftoverResult"
}Community
Evidence
Recent observations
verifiedversion not recorded6 tools