gnomad-genetics-mcp-server: get coverage
gnomad_get_coverageFetch 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. gnomAD publishes no coverage for subsets, so a subset dataset reads its parent release (gnomad_r4_non_ukb reads gnomad_r4) over all the parent’s samples: coverage_dataset names the release read, and a notice says so. Echoes the effective dataset and build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/
Tool call template
This tool declares no required parameters. Add optional parameters from the input schema as needed.
{
"id": 1,
"jsonrpc": "2.0",
"method": "tools/call",
"params": {
"arguments": {},
"name": "gnomad_get_coverage"
}
}Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gene | No | 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. | |
| region | No | 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. | |
| dataset | No | gnomAD dataset, default gnomad_r4: gnomad_r4 and its subset gnomad_r4_non_ukb (GRCh38); gnomad_r3 and its subsets gnomad_r3_controls_and_biobanks, gnomad_r3_non_cancer, gnomad_r3_non_neuro, gnomad_r3_non_topmed, gnomad_r3_non_v2 (GRCh38); gnomad_r2_1 and its subsets gnomad_r2_1_controls, gnomad_r2_1_non_cancer, gnomad_r2_1_non_neuro, gnomad_r2_1_non_topmed (GRCh37); exac (GRCh37). A subset keeps only part of its parent release's samples (non_cancer leaves out cancer-study samples, non_ukb UK Biobank's) and can leave a callset unchanged: gnomad_r4_non_ukb genome counts equal gnomad_r4's, and gnomad_r2_1_non_cancer genome counts equal gnomad_r2_1's. No subset publishes joint data, and gnomAD publishes no subset coverage or constraint, so those come from the parent. Echoed in output. | |
| transcript_id | No | Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted. | |
| coverage_source | No | Restrict to one coverage track. Omit to return every available track. | |
| reference_genome | No | Reference build. Derived from dataset when omitted: GRCh38 for gnomad_r4, gnomad_r3, and their subsets; GRCh37 for gnomad_r2_1, its subsets, and exac. If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| error | No | Present when the call failed. Absent on success. | |
| notice | No | Disclosure that a subset dataset was read from its parent release, and of missing target bases, missing supported tracks, or an explicitly requested unsupported track. Missing data leaves callability unknown. | |
| target | No | The resolved target (gene symbol/ID, transcript ID, or region) the coverage describes. | |
| dataset | No | Effective gnomAD dataset. | |
| summaries | No | Per-track coverage summaries (exome and/or genome). | |
| target_kind | No | Which target type was queried. | |
| coverage_dataset | No | The gnomAD release the coverage was read from: dataset itself for a release, the parent release for a subset (gnomad_r4 for gnomad_r4_non_ukb, gnomad_r3 for the gnomad_r3 subsets, gnomad_r2_1 for the gnomad_r2_1 subsets), since gnomAD publishes no subset coverage. | |
| reference_genome | No | Effective reference build. |