GeneBe
Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only.
我該用這個嗎
品質與安全性
A
根據工具定義與協定合規性的自動化分析。
上下文成本
~5,264Token（工具定義）
~8.9 KB典型回應大小
顯著的注意力影響（128k 上下文的 4.11%）
這是每次將伺服器的工具載入模型上下文時所消耗的約略 token 數量。數量越高，可用於其他工作的注意力就越少。
安裝
一鍵安裝
將以下內容加入你的 `claude_desktop_config.json` 檔案：
{
"mcpServers": {
"genebe-mcp": {
"url": "https://mcp.genebe.net/v1/mcp"
}
}
}遠端端點
https://mcp.genebe.net/v1/mcpstreamable-http它能做什麼
工具清單
工具（6）
🟢 唯讀🟡 寫入🔴 刪除⚪ 未知
🟢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.
輸入結構描述
{
"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"
}輸出結構描述
{
"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": "#/$defs/GeneVerdict"
},
"title": "Per Gene",
"type": "array"
},
"disclaimer": {
"default": "For research use only. Not a diagnosis; results must be reviewed by a qualified specialist before any clinical use.",
"title": "Disclaimer",
"type": "string"
}
},
"required": [
"classification",
"points",
"criteria",
"per_gene"
],
"title": "Verdict",
"type": "object"
}
},
"title": "AnnotationResult"
}🟢explain_acmg_decision_path(variant, genome, tree, version)
Explain step by step why each classification criterion did or did not apply to a variant. Use after annotate_variant when the user asks "why was this classified that way?". Returns an ASCII rendering of the decision tree with the evaluated conditions. By default it explains the germline ACMG verdict that annotate_variant returns; the somatic trees 'oncogenicity' (2022) and 'acgs-uk-onco' (2025) can be requested explicitly. Research use only.
輸入結構描述
{
"type": "object",
"properties": {
"variant": {
"description": "The variant, in any notation accepted by annotate_variant.",
"title": "Variant",
"type": "string"
},
"genome": {
"default": "hg38",
"description": "Genome build of coordinate input.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "Genome",
"type": "string"
},
"tree": {
"default": "germline",
"description": "Decision tree: 'germline' (default), 'oncogenicity' or 'acgs-uk-onco'.",
"title": "Tree",
"type": "string"
},
"version": {
"default": "2019",
"description": "Tree version: germline 2019 (default), oncogenicity 2022, acgs-uk-onco 2025.",
"title": "Version",
"type": "string"
}
},
"required": [
"variant"
],
"title": "explain_acmg_decision_pathArguments"
}輸出結構描述
{
"type": "object",
"properties": {
"variant": {
"$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.
輸入結構描述
{
"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"
}輸出結構描述
{
"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"
],
"$defs": {
"VariantCoordinates": {
"properties": {
"genome": {
"title": "Genome",
"type": "string"
},
"chr": {
"title": "Chr",
"type": "string"
},
"pos": {
"description": "1-based VCF position",
"title": "Pos",
"type": "integer"
},
"ref": {
"title": "Ref",
"type": "string"
},
"alt": {
"title": "Alt",
"type": "string"
}
},
"required": [
"genome",
"chr",
"pos",
"ref",
"alt"
],
"title": "VariantCoordinates",
"type": "object"
}
},
"title": "ConvertResult"
}🟢get_variant_effects(variant, genome)
List a variant's predicted molecular consequences on every overlapping transcript. Returns per-transcript HGVS (c. and p.), consequence terms (e.g. missense_variant) and impact, most severe and MANE Select transcripts first. Lightweight: no frequencies or classification.
輸入結構描述
{
"type": "object",
"properties": {
"variant": {
"description": "The variant, in any notation accepted by annotate_variant.",
"title": "Variant",
"type": "string"
},
"genome": {
"default": "hg38",
"description": "Genome build of coordinate input.",
"enum": [
"hg19",
"hg38",
"t2t"
],
"title": "Genome",
"type": "string"
}
},
"required": [
"variant"
],
"title": "get_variant_effectsArguments"
}輸出結構描述
{
"type": "object",
"properties": {
"variant": {
"$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.
輸入結構描述
{
"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"
}輸出結構描述
{
"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.
輸入結構描述
{
"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"
}輸出結構描述
{
"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"
}社群
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