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gnomad-genetics-mcp-server

gnomad-genetics-mcp-server: get coverage

gnomad_get_coverage
Read-onlyIdempotent

Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each depth threshold (1× through 100×), separated by exome and genome track. gnomAD reports coverage in buckets: 1 bp for a region spanning under 850 bp, wider for larger targets (bucket_size), and a gene or transcript is summarized over its exons ±75 bp, not its introns. Use this to disambiguate a true absent variant from an uncallable position: a variant missing from a well-covered region is informative, while one missing from a poorly-covered region is not. Supply exactly one of gene, transcript_id, or region. The optional coverage_source narrows to one track; by default both available tracks are returned. Echoes the effective dataset and build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
geneNoGene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted.
regionNoGenomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served) and a span (stop − start) under 2,500,000 bp. Mutually exclusive with gene and transcript_id.
datasetNognomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
transcript_idNoEnsembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.
coverage_sourceNoRestrict to one coverage track. Omit to return every available track.
reference_genomeNoReference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
noticeNoGuidance when no coverage data is available for the target.
targetNoThe resolved target (gene symbol/ID, transcript ID, or region) the coverage describes.
datasetNoEffective gnomAD dataset.
summariesNoPer-track coverage summaries (exome and/or genome).
target_kindNoWhich target type was queried.
reference_genomeNoEffective reference build.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed15 schema fields changed
    • addedOutput schema / properties / summaries / items / properties / bucket_count
      Added value: +{
      +  "description": "Number of gnomAD coverage buckets summarized: every returned bucket overlapping the target bases. gnomAD returns every bucket between the first and last record of a track, so an empty bucket inside that span counts as zero depth; buckets past the outermost records are not returned and not counted.",
      +  "type": "number"
      +}
    • addedOutput schema / properties / summaries / items / properties / bucket_size
      Added value: +{
      +  "description": "Width of each gnomAD coverage bucket in bp: 1 for a region spanning under 850 bp, otherwise about 1/500 of the queried size. Depth and fraction values describe buckets, not single bases.",
      +  "type": "number"
      +}
    • changedOutput schema / properties / summaries / items / properties / fraction_over_1 / description
      Previous value: -"Mean fraction of samples covered at ≥1×; null when no data."New value: +"Fraction of samples covered at ≥1×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / fraction_over_10 / description
      Previous value: -"Mean fraction of samples covered at ≥10×; null when no data."New value: +"Fraction of samples covered at ≥10×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / fraction_over_100 / description
      Previous value: -"Mean fraction of samples covered at ≥100×; null when no data."New value: +"Fraction of samples covered at ≥100×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / fraction_over_15 / description
      Previous value: -"Mean fraction of samples covered at ≥15×; null when no data."New value: +"Fraction of samples covered at ≥15×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / fraction_over_20 / description
      Previous value: -"Mean fraction of samples covered at ≥20×; null when no data."New value: +"Fraction of samples covered at ≥20×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / fraction_over_25 / description
      Previous value: -"Mean fraction of samples covered at ≥25×; null when no data."New value: +"Fraction of samples covered at ≥25×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / fraction_over_30 / description
      Previous value: -"Mean fraction of samples covered at ≥30×; null when no data."New value: +"Fraction of samples covered at ≥30×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / fraction_over_5 / description
      Previous value: -"Mean fraction of samples covered at ≥5×; null when no data."New value: +"Fraction of samples covered at ≥5×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / fraction_over_50 / description
      Previous value: -"Mean fraction of samples covered at ≥50×; null when no data."New value: +"Fraction of samples covered at ≥50×, averaged over the summarized buckets (gnomAD rounds each bucket's fraction up to the next 0.01); null when no data."
    • changedOutput schema / properties / summaries / items / properties / mean_depth / description
      Previous value: -"Mean read depth averaged across positions; null when no data."New value: +"Mean read depth: the average of the summarized buckets’ mean depths; null when no data."
    • changedOutput schema / properties / summaries / items / properties / median_depth / description
      Previous value: -"Median read depth across positions; null when no data."New value: +"Median, across the summarized buckets, of each bucket’s depth (the average of its per-base medians); null when no data."
    • changedOutput schema / properties / summaries / items / properties / positions / description
      Previous value: -"Number of base positions summarized across the target."New value: +"Target bases inside the summarized buckets: of start..stop for a region, of the exons ±75 bp for a gene or transcript. Falls short of the target when the track has no records at its edges (typically outside the exome capture); those bases are left out, not counted as zero depth."
    • changedOutput schema / properties / summaries / items / required
      Previous value: -[
      -  "source",
      -  "positions",
      -  "mean_depth",
      -  "median_depth",
      -  "fraction_over_1",
      -  "fraction_over_5",
      -  "fraction_over_10",
      -  "fraction_over_15",
      -  "fraction_over_20",
      -  "fraction_over_25",
      -  "fraction_over_30",
      -  "fraction_over_50",
      -  "fraction_over_100"
      -]New value: +[
      +  "source",
      +  "positions",
      +  "bucket_count",
      +  "bucket_size",
      +  "mean_depth",
      +  "median_depth",
      +  "fraction_over_1",
      +  "fraction_over_5",
      +  "fraction_over_10",
      +  "fraction_over_15",
      +  "fraction_over_20",
      +  "fraction_over_25",
      +  "fraction_over_30",
      +  "fraction_over_50",
      +  "fraction_over_100"
      +]
  2. Changed5 schema fields changed
    • changedInput schema / properties / gene / description
      Previous value: -"Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mutually exclusive with transcript_id and region; blank means omitted."New value: +"Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted."
    • changedInput schema / properties / region / anyOf
      Previous value: -[
      -  {
      -    "const": "",
      -    "type": "string"
      -  },
      -  {
      -    "description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852).",
      -    "pattern": "^[0-9XYM]+-\\d+-\\d+$",
      -    "type": "string"
      -  }
      -]New value: +[
      +  {
      +    "const": "",
      +    "type": "string"
      +  },
      +  {
      +    "description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852) on chromosome 1–22, X, or Y, optional chr prefix.",
      +    "pattern": "^(?:chr)?[0-9A-Z]+-\\d+-\\d+$",
      +    "type": "string"
      +  }
      +]
    • changedInput schema / properties / region / description
      Previous value: -"Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852). Mutually exclusive with gene and transcript_id."New value: +"Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served) and a span (stop − start) under 2,500,000 bp. Mutually exclusive with gene and transcript_id."
    • changedOutput schema / properties / error / properties / data / properties / reason / description
      Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_target`: Not exactly one of gene, transcript_id, or region was supplied. `incoherent_build`: reference_genome was supplied but does not match the dataset. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_target`: Not exactly one of gene, transcript_id, or region was supplied. `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_region`: The region names a chromosome outside 1–22, X, Y, or breaks the coordinate bounds. `region_too_large`: The region spans 2,500,000 bp or more, beyond what gnomAD summarizes at once. `mitochondrial_unsupported`: The gene, transcript, or region is on the mitochondrial chromosome (M or MT). `graphql_error`: gnomAD rejected the coverage query with a GraphQL error. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry. `upstream_timeout`: Every attempt to reach gnomAD timed out. `upstream_access`: gnomAD refused the request (access denied). `invalid_upstream_response`: gnomAD kept answering with a response that failed validation. Other values are possible when a failure originates below the handler."
    • changedOutput schema / properties / error / properties / data / properties / reason / examples
      Previous value: -[
      -  "invalid_target",
      -  "incoherent_build"
      -]New value: +[
      +  "invalid_target",
      +  "incoherent_build",
      +  "invalid_region",
      +  "region_too_large",
      +  "mitochondrial_unsupported",
      +  "graphql_error",
      +  "upstream_unavailable",
      +  "upstream_timeout",
      +  "upstream_access",
      +  "invalid_upstream_response"
      +]
  3. Changed5 schema fields changed
    • addedInput schema / properties / gene / anyOf
      Added value: +[
      +  {
      +    "description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.",
      +    "minLength": 2,
      +    "type": "string"
      +  },
      +  {
      +    "description": "Blank — the gene is treated as omitted.",
      +    "maxLength": 0,
      +    "type": "string"
      +  }
      +]
    • changedInput schema / properties / gene / description
      Previous value: -"Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene."New value: +"Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mutually exclusive with transcript_id and region; blank means omitted."
    • removedInput schema / properties / gene / minLength
      Removed value: -2
    • removedInput schema / properties / gene / type
      Removed value: -"string"
    • changedInput schema / properties / transcript_id / description
      Previous value: -"Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region."New value: +"Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted."
  4. Changed22 schema fields changed
    • removedOutput schema / properties / summaries / items / properties / fraction_over_1 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_1 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / fraction_over_10 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_10 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / fraction_over_100 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_100 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / fraction_over_15 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_15 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / fraction_over_20 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_20 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / fraction_over_25 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_25 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / fraction_over_30 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_30 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / fraction_over_5 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_5 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / fraction_over_50 / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / fraction_over_50 / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / mean_depth / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / mean_depth / type
      Added value: +[
      +  "number",
      +  "null"
      +]
    • removedOutput schema / properties / summaries / items / properties / median_depth / anyOf
      Removed value: -[
      -  {
      -    "type": "number"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]
    • addedOutput schema / properties / summaries / items / properties / median_depth / type
      Added value: +[
      +  "number",
      +  "null"
      +]
  5. First observed

TDQS

A4.6/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already cover the safe-read profile (readOnly, idempotent, openWorld), and the description adds substantial non-obvious behavior: coverage bucket sizing (1 bp under 850 bp, wider otherwise), gene/transcript summarization over exons ±75 bp excluding introns, and echoing of dataset/build. This is real context beyond the structured fields.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loads the resource and return shape, then the usage rationale, then constraints and source attribution. Dense and mostly earns its place, though the bucket-size and ±75 bp detail is lengthy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists so return values need not be restated, and the description covers selection, mutual-exclusivity, defaults, and dataset/build echoing. Nothing an agent needs to invoke it correctly is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so a baseline of 3 applies, but the description adds meaning beyond the schema: the mutual-exclusivity rule across gene/transcript/region, the exome/genome narrowing of coverage_source, and the default of returning both tracks. Useful semantic layering over an already-documented schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb+resource (fetch gnomAD sequencing-coverage summary) and the exact scope (gene, transcript, or region), enumerating what is returned (mean/median depth, fraction covered at 1x-100x, exome vs genome). An agent can clearly separate this from siblings like gnomad_get_gene_constraint or gnomad_get_variant.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives an explicit use case — disambiguating a true absent variant from an uncallable position — and enforces 'exactly one of gene, transcript_id, or region' plus default behavior for coverage_source. It does not name a sibling tool as the alternative, so it falls short of full when/when-not routing.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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