GeneBe
Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only.
¿Debería usar esto?
Calidad y seguridad
A
Basado en el análisis automatizado de las definiciones de herramientas y el cumplimiento del protocolo.
Costo de contexto
~5,264Tokens (definiciones de herramientas)
~8.9 KBTamaño de respuesta típico
Impacto significativo en la atención (4.11% del contexto de 128k)
Este es el número aproximado de tokens que se consumen cada vez que las herramientas del servidor se cargan en el contexto de un modelo. Los recuentos más altos reducen la atención disponible para otras tareas.
Instalar
Instalación con un clic
Agrega esto a tu archivo `claude_desktop_config.json`:
{
"mcpServers": {
"genebe-mcp": {
"url": "https://mcp.genebe.net/v1/mcp"
}
}
}Puntos de conexión remotos
https://mcp.genebe.net/v1/mcpstreamable-httpQué puede hacer
Inventario de herramientas
Herramientas (6)
🟢 Solo lectura🟡 Escritura🔴 Eliminación⚪ Desconocido
🟢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.
Esquema de entrada
{
"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"
}Esquema de salida
{
"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": "#/$defs/GeneVerdict"
},
"title": "Per Gene",
"type": "array"
},
"disclaimer": {
"default": "For research use only. Not a diagnosis; results must be reviewed by a qualified specialist before any clinical use.",
"title": "Disclaimer",
"type": "string"
}
},
"required": [
"classification",
"points",
"criteria",
"per_gene"
],
"title": "Verdict",
"type": "object"
}
},
"title": "AnnotationResult"
}🟢explain_acmg_decision_path(variant, genome, tree, version)
Explain step by step why each classification criterion did or did not apply to a variant. Use after annotate_variant when the user asks "why was this classified that way?". Returns an ASCII rendering of the decision tree with the evaluated conditions. By default it explains the germline ACMG verdict that annotate_variant returns; the somatic trees 'oncogenicity' (2022) and 'acgs-uk-onco' (2025) can be requested explicitly. Research use only.
Esquema de entrada
{
"type": "object",
"properties": {
"variant": {
"description": "The variant, in any notation accepted by annotate_variant.",
"title": "Variant",
"type": "string"
},
"genome": {
"default": "hg38",
"description": "Genome build of coordinate input.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "Genome",
"type": "string"
},
"tree": {
"default": "germline",
"description": "Decision tree: 'germline' (default), 'oncogenicity' or 'acgs-uk-onco'.",
"title": "Tree",
"type": "string"
},
"version": {
"default": "2019",
"description": "Tree version: germline 2019 (default), oncogenicity 2022, acgs-uk-onco 2025.",
"title": "Version",
"type": "string"
}
},
"required": [
"variant"
],
"title": "explain_acmg_decision_pathArguments"
}Esquema de salida
{
"type": "object",
"properties": {
"variant": {
"$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.
Esquema de entrada
{
"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"
}Esquema de salida
{
"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"
],
"$defs": {
"VariantCoordinates": {
"properties": {
"genome": {
"title": "Genome",
"type": "string"
},
"chr": {
"title": "Chr",
"type": "string"
},
"pos": {
"description": "1-based VCF position",
"title": "Pos",
"type": "integer"
},
"ref": {
"title": "Ref",
"type": "string"
},
"alt": {
"title": "Alt",
"type": "string"
}
},
"required": [
"genome",
"chr",
"pos",
"ref",
"alt"
],
"title": "VariantCoordinates",
"type": "object"
}
},
"title": "ConvertResult"
}🟢get_variant_effects(variant, genome)
List a variant's predicted molecular consequences on every overlapping transcript. Returns per-transcript HGVS (c. and p.), consequence terms (e.g. missense_variant) and impact, most severe and MANE Select transcripts first. Lightweight: no frequencies or classification.
Esquema de entrada
{
"type": "object",
"properties": {
"variant": {
"description": "The variant, in any notation accepted by annotate_variant.",
"title": "Variant",
"type": "string"
},
"genome": {
"default": "hg38",
"description": "Genome build of coordinate input.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "Genome",
"type": "string"
}
},
"required": [
"variant"
],
"title": "get_variant_effectsArguments"
}Esquema de salida
{
"type": "object",
"properties": {
"variant": {
"$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.
Esquema de entrada
{
"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"
}Esquema de salida
{
"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.
Esquema de entrada
{
"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"
}Esquema de salida
{
"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"
}Comunidad
Evidencia
Observaciones recientes
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