BRaVa MCP
BRaVa MCP is a read-only server for exploring BRaVa rare-variant gene-based and single-variant association results, mostly with local SQL and some HTTP-fetched variant data.
Run read-only SQL over 61.8 million gene-level rows: every gene × trait × variant mask × MAF cutoff × ancestry, including Burden/SKAT/SKAT-O p-values, beta/SE, and heterogeneity.
Get the
schematool with tables, columns, runnable query recipes, analysis vocabulary, significance thresholds, and pitfalls that prevent scientifically wrong queries.Use
gene_phenotype_detailto check whether a gene–trait association replicates across ancestries/biobanks, screening a single pair or a comma-separated hit list.Use
variantsto fetch single-variant results genome-wide for a trait, restrict to one gene or chromosome, filter by p-value, and link to gnomAD for allele frequencies.Answer scientific questions such as most pleiotropic genes, ancestry-specific signals, and significant associations hidden in pooled strata.
Supports local cached operation, stdio or HTTP transport, and offline testing/evaluation workflows.
Emphasises careful interpretation: effect sizes belong to the Burden test, the synonymous mask is a calibration control, ancestry strata overlap, and exact-zero p-values are the strongest signals.
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@BRaVa MCPScreen PCSK9, LDLR, APOB for LDLC replication"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
BRaVa MCP
An MCP server for the Biobank Rare Variant Analysis (BRaVa) consortium's association results: rare coding-variant, gene-based tests meta-analysed across ~1.2M individuals from 10 global biobanks, 44 harmonised traits, 7 ancestry strata.
Summary statistics only. Not for clinical use.
SQL over the whole table
query runs read-only SQL against all 61,791,444 gene-level rows: every gene x
trait x variant-mask x MAF-cutoff x ancestry cell, with the Burden, SKAT and
SKAT-O p-values, the effect size and its standard error, and the cross-cohort
heterogeneity test. The database is local, so a query costs no network.
-- what does this gene do
SELECT trait, mask, p_skato, beta FROM results
WHERE gene='PCSK9' AND ancestry='All' AND mask<>'synonymous'
ORDER BY p_skato LIMIT 20
-- most pleiotropic genes
SELECT gene, count(DISTINCT trait) traits FROM results
WHERE ancestry='All' AND p_skato < 1.39e-7 GROUP BY gene ORDER BY traits DESC
-- what a European-only study would have missed
SELECT a.gene, a.trait, a.p_skato FROM results a
WHERE a.ancestry='AFR' AND a.p_skato < 2.5e-6 AND NOT EXISTS (
SELECT 1 FROM results e WHERE e.ancestry='EUR'
AND e.gene_idx=a.gene_idx AND e.pheno=a.pheno AND e.p_skato < 2.5e-6)Related MCP server: gwas-mcp
Tools
Tool | What it is for |
| Read-only SQL over the whole gene-level table |
| Tables, columns, runnable recipes, and the traps that make a valid query scientifically wrong. Read this first |
| Cross-ancestry replication for a gene-trait pair, or a screen over a hit list |
| Single-variant results, genome-wide for a trait or inside one gene |
Why the other three exist.
gene_phenotype_detail computes the concordance count over the five
superpopulations only, excluding All and non_EUR, which pool the same
individuals. A query that aggregates over every ancestry double-counts.
variants fetches over HTTP. The variant-level release is a separate upstream
format of 3.09 GiB across ~176,000 objects, against 1.19 GiB for the gene-level
data, and it is not included in the local database.
schema() returns the tables and columns, runnable query templates, and ten
pitfalls: effect sizes belong to a different test than the p-value beside them,
one mask is a calibration control rather than a biological category, ancestry
strata overlap, a p-value of exactly zero is the strongest result rather than a
missing one, and six more. Read it before writing SQL.
The database
873 MB, published as a
release asset and
downloaded once into ~/.cache/brava-mcp/ at first use. Cloning this repo costs
3.9 MB.
Built by etl/build_db.py from the 280 published phenotype/{P}.{ANC}.json
files. Those carry the same data as the 19,541 per-gene files, so the pivot is
chosen for politeness: 280 requests against 19,541 for identical coverage, once,
rather than one per gene consulted forever. Class B operations are the scarce
resource on the upstream free tier; egress is free on R2.
Sorted on the low-cardinality key columns and built without ART indexes: 2.49 GB with indexes, 1.75 GB without, 0.87 GB sorted. No index is missed, because these are filtered scans and DuckDB's zonemaps already serve them. Every query above returns in under 70 ms.
Running it
make sync # install
make db # download the published database (873 MB, once)
make test # offline suite
make test-all # + live-data checks
make eval # 14 benchmark questions, answers derived independently
make serve # HTTP daemon on :3163
uv run python server.py # stdioRebuild the database from upstream with uv run python etl/build_db.py
(~200 s: 120 s of downloads, 76 s of loading, then the sorted compaction).
Variable | Default | Purpose |
|
|
|
|
| daemon port |
| the release asset | where to fetch the database |
|
| local database |
| upstream R2 | variant-level files |
Reading the results
beta > 0 increases risk (binary traits) or the trait value (quantitative).
betaandsealways come from the inverse-variance-weighted Burden meta-analysis, including on rows where you readp_skato. There is no SKAT-O effect size.SKAT-O is the primary omnibus test. Burden is most powerful when a gene's variants point the same way; SKAT when they are mixed.
The
synonymousmask is a calibration control. A significant synonymous result indicates residual test inflation, not biology.Thresholds from the flagship paper: gene × mask Bonferroni 1.39e-7, gene-level Cauchy 2.5e-6, variant-level 1.82e-8.
BRaVa carries no allele frequencies and no common-variant GWAS. Variant rows link to gnomAD for the former.
schema() returns all of this, plus five more traps, alongside the columns.
Evaluation
evals/questions.json holds fourteen questions, all fourteen resolved directly
from the raw upstream files by evals/resolve_golds.py, which imports nothing
from brava, so the benchmark cannot agree with a decoding bug and doubles as an
upstream-drift detector.
evals/selfcheck.py walks each question through the tools: currently 14/14, a
median of one call per question, and zero outbound HTTP requests for the whole
set. It checks each question's evidence (the values the tools must return) and
never its answer, because several answers are conclusions no string match can
verify. So it proves the data is reachable and at what cost, not that a model
reaches the right conclusion; that half needs a model-in-the-loop runner and is
still missing.
Traffic
Gene-level questions are local, so they cost the upstream project nothing at all.
Only variants fetches, and each file is cached permanently. Building the
database costs 280 requests, once. See
nikbaya/brava_browser#1 for
the conversation with the upstream author.
Citation
Palmer, Hill, Hodgson, et al. Rare variant association analyses across 10 global biobanks. medRxiv (2026). doi:10.64898/2026.05.21.26353759
The database is derived from that release via the BRaVa browser's published files, and is redistributed under the browser's MIT licence.
Licence
MIT.
Available Tools
4 toolsgene_phenotype_detailBRead-onlyIdempotent
Does a gene-trait association replicate across ancestries and biobanks?
BRaVa's distinctive view, and a tool rather than a documented query because the concordance count has to exclude the two pooled strata ('All' and 'non_EUR') that contain the same individuals as the ones being counted. The obvious SQL double-counts and looks entirely reasonable.
Pass a comma-separated list to screen a whole hit list at once: one gene at a time costs a call each, the list form returns a verdict per gene. Verdicts separate "underpowered" from "discordant", which is the distinction that matters when a stratum is fifteen times smaller than another.
| Name | Required | Description | Default |
|---|---|---|---|
| maf | No | "<0.1%" (default) or "<0.01%". | <0.1% |
| gene | Yes | Gene symbol or Ensembl id, or a comma-separated list of them. | |
| mask | No | Variant annotation mask (default "pLoF | damaging missense"). | pLoF | damaging missense |
| test | No | Burden, SKAT or SKAT-O (default SKAT-O). | SKAT-O |
| phenotype | Yes | Trait id or name. |
Output Schema
| Name | Required | Description |
|---|---|---|
| result | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, setting a baseline for safety. The description adds context beyond annotations: it explains why this is a tool (SQL double-counting) and describes the verdict types. This is helpful but not exhaustive—there is no mention of rate limits, authentication needs, or what happens if inputs are invalid. The description adds some behavioral insight but falls short of full transparency.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is verbose and includes extraneous technical reasoning about SQL double-counting and the tool's origin. While informative, the first three sentences could be condensed. The key actionable information (handling lists, verdict meanings) appears only in the last two sentences. The structure lacks front-loading of essential details, making it less efficient for an AI agent.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the output schema exists (context confirms), the description does not need to detail return values. It explains the tool's purpose, input batch behavior, and verdict semantics, which suffices for most use cases. However, it omits specifics about supported biobanks, ancestry strata, or example phenotype IDs. The description is adequate for an expert but could be more complete for general AI consumption.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema covers all 5 parameters with descriptions (100% coverage), so the baseline is 3. The description adds extra value: it notes that the 'gene' parameter accepts a comma-separated list and that using a list returns a verdict per gene. It also clarifies the default for 'maf' and 'mask'. This goes beyond the schema, improving parameter understanding for batch usage.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description opens with a clear question defining the tool's purpose: 'Does a gene-trait association replicate across ancestries and biobanks?' This directly states the function. It also distinguishes itself as a specialized view that handles a SQL double-counting issue, which helps set it apart from generic query tools like the sibling 'query'. However, the purpose is embedded within technical reasoning, slightly reducing clarity for a general AI agent.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides some usage advice: passing a comma-separated list to screen multiple genes, noting that one gene at a time costs a call each. It also explains the verdict distinction between 'underpowered' and 'discordant'. However, it does not explicitly say when to use this tool versus its siblings ('query', 'schema', 'variants') or when not to use it. The guidance is present but implicit and incomplete.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
queryARead-onlyIdempotent
Run read-only SQL over the whole BRaVa gene-level results table.
61.8 million rows: every gene x trait x variant-mask x MAF-cutoff x ancestry cell, with the Burden, SKAT and SKAT-O p-values, the effect size and its standard error, and the cross-cohort heterogeneity test. Local, so a query costs no network.
Call schema() first. It returns the tables, the columns, worked query
templates, and the semantic traps that make a syntactically valid query
scientifically wrong here. Several of them invert the answer rather than
degrade it.
Query the results view rather than the raw tables: it exposes p-values
instead of -log10, and labels instead of integer codes, so the obvious query
is also the correct one.
| Name | Required | Description | Default |
|---|---|---|---|
| sql | Yes | One read-only statement (SELECT / WITH / DESCRIBE / SHOW / EXPLAIN). Combine steps with a CTE rather than sending several statements. | |
| max_rows | No | Rows returned (default 50, capped 500). The response is also capped at 25,000 characters, so select the columns you need. |
Output Schema
| Name | Required | Description |
|---|---|---|
| result | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, so the description's behavioral burden is lower. The description adds value by disclosing the exact size of the table ('61.8 million rows'), the cost profile ('local, so a query costs no network'), and the fact that results are capped (25,000 characters, max rows 500). This goes beyond basic safety disclosure to provide performance expectations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is well-structured with a clear introductory sentence, a list of table contents, a callout to call schema() first, and a recommendation to use the results view. Every sentence adds value. It could be slightly more concise by removing the exact row count and focusing on the most critical guidance, but it's not overly verbose.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the complexity of the domain (61.8 million rows, multiple dimensions per cell), the rich annotations (readOnly, openWorld, idempotent), a fully described 2-parameter schema, and the presence of an output schema, the description is remarkably complete. It explains the exact contents, potential pitfalls (semantic traps), and best practices. There is no need to discuss return values since an output schema exists.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema already provides clear descriptions for both parameters (sql and max_rows) with examples and constraints. Schema description coverage is 100%, so the baseline is 3. The description does not add meaning beyond what the schema provides, as the schema already explains the allowed SQL statements, default row count, and character limit. The description's mention of capping (500 rows, 25,000 chars) is redundant with the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool runs 'read-only SQL over the whole BRaVa gene-level results table.' It specifies the verb ('query'), resource ('BRaVa gene-level results table'), and scope ('read-only SQL'). While the name 'query' is generic, the description distinguishes it from siblings by specifying the exact domain (BRaVa) and table type (gene-level results), making it clear what this tool does compared to 'variant' or 'schema'.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explicitly advises to 'call `schema()` first' to understand the correct tables, columns, and semantic traps. It warns about semantic traps that can 'invert the answer.' It recommends querying the `results` view instead of raw tables. This provides explicit when-to-use guidance and a prerequisite action (calling schema()), which is excellent for avoiding misuse.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
schemaARead-onlyIdempotent
The tables, the query templates, and the traps. Read this before querying.
Returns the shipped tables with their columns and row counts, worked queries for the questions people actually ask, the analysis vocabulary (masks, MAF cutoffs, tests, significance thresholds), and a list of ways a correct-looking query gives a wrong answer on this data. That list is not boilerplate: it covers effect sizes that belong to a different test than the p-value beside them, a mask that is a calibration control rather than a biological category, ancestry strata that overlap, and p-values of exactly zero that mean the most significant result rather than a missing one.
Returns: tables, columns, recipes, vocabulary, thresholds and pitfalls.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
Output Schema
| Name | Required | Description |
|---|---|---|
| result | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already provide readOnlyHint, openWorldHint, and idempotentHint, which signal safety and non-mutating behavior. The description adds significant behavioral value beyond these: it details specific pitfalls (e.g., effect sizes mismatched to p-values, overlapping ancestry strata, p-values of exactly zero) that would otherwise be opaque. It also describes the return structure comprehensively.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is moderately concise but slightly verbose in the second paragraph (listing all pitfalls could be slightly tighter). However, it front-loads the critical usage instruction ('Read this before querying') and the return list. Every sentence adds value and earns its place by providing context not in structured fields.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool has 0 parameters, no nested objects, and a likely output schema (mentioned but not provided here), the description is remarkably complete. It covers purpose, usage timing, return structure, and even specific pitfalls. The contextual signals (parameter count 0, schema coverage 100%) confirm no gaps need filling.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The tool has 0 parameters and schema description coverage is 100% (though empty schema). The description adds no parameter details because there are none, but this is appropriate and complete for a parameterless tool. No further explanation needed.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool returns 'tables, columns, recipes, vocabulary, thresholds and pitfalls' – a specific resource (schema/metadata) with a distinct verb 'returns'. It distinguishes itself from siblings like 'query' and 'variants' by describing this as a metadata discovery tool rather than a data retrieval tool.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explicitly says 'Read this before querying,' setting a clear usage context: this should be called before using sibling tools (e.g., 'query') to understand the data structure, pitfalls, and analysis vocabulary. It implies when-not-to-use by framing itself as preparatory, not transactional.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
variantsARead-onlyIdempotent
Single-variant results for a trait, genome-wide or inside one gene.
Drops below the gene-level burden tests to the individual variants carrying a
signal. Without gene this ranks the whole genome for the trait; with gene
it restricts to that gene and adds the per-biobank effect-direction tally,
the cross-biobank replication evidence.
Still fetched over HTTP rather than shipped in the database: the variant-level format is a separate, actively changing upstream release, an order of magnitude larger than the gene-level table, and rebuilt often enough that a local copy would be stale within the week. Each file is cached permanently once fetched.
Each row links to gnomAD, where population allele frequencies live.
| Name | Required | Description | Default |
|---|---|---|---|
| gene | No | Restrict to one gene. Omit for the genome-wide scan. | |
| chrom | No | Restrict the genome-wide scan to one chromosome ("2", "X"). | |
| limit | No | Max rows (default 25). | |
| max_p | No | p-value ceiling. The variant-level threshold is 1.82e-8. | |
| offset | No | Skip this many rows, to page through a long result set. | |
| ancestry | No | All (cross-ancestry meta, default) or a specific stratum. Only meaningful together with `gene`. | All |
| phenotype | Yes | Trait id or name. |
Output Schema
| Name | Required | Description |
|---|---|---|
| result | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description adds rich behavioral context beyond the annotations: explains the HTTP fetch mechanism, reasons for not storing the data locally (large size, frequent upstream rebuilds), caching behavior (permanent caching after first fetch), and links to external data (gnomAD). This goes far beyond the readOnlyHint, openWorldHint, and idempotentHint annotations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is structured into three clear paragraphs, front-loaded with the core purpose. It contains some explanatory detail (e.g., HTTP fetch rationale) that is valuable but slightly verbose. Overall, each sentence contributes to understanding the tool's behavior and usage.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With an output schema present, the description need not detail return values. It covers purpose, modes, differentiation from siblings, caching, and external references. It does not explicitly mention pagination or error handling, but the schema descriptions for limit/offset and context signals provide that. The description is largely complete for a read-only data retrieval tool.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, providing baseline 3. The description adds significant value for the 'gene' parameter by explaining it enables additional per-biobank effect-direction and cross-biobank replication evidence. It also reinforces the role of 'max_p' implicitly through mention of the threshold. For other parameters, the schema descriptions suffice.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool returns 'single-variant results for a trait, genome-wide or inside one gene', explicitly distinguishing it from gene-level burden tests (likely a sibling tool). It uses a specific verb (returns/fetches) and resource (variants), and explains the two distinct modes of operation.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explains when to use genome-wide vs per-gene mode and contrasts with gene-level burden tests. It implies usage context well but does not explicitly state 'when not to use' or name alternative tools. The guidance on caching and HTTP fetch provides operational context.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Tool Schema Changelog
Recent tool additions, removals, and schema changes observed during successful MCP inspections. Dates show when Glama detected each change.
4 tool updates
v0.1.0- First observed
gene_phenotype_detail - First observed
query - First observed
schema - First observed
variants
TDQS
Each tool has a distinct role: schema provides metadata and pitfalls, query runs arbitrary SQL, gene_phenotype_detail performs cross-ancestry replication analysis, and variants retrieves single-variant results. There is no overlap in functionality, and descriptions clearly differentiate use cases.
All tool names use lowercase and underscores, but they mix single-word verbs ('query', 'schema') and descriptive multi-word nouns ('gene_phenotype_detail', 'variants'). While the style is consistent (underscore_case), the pattern varies between imperative and descriptive, which is acceptable but not perfectly uniform.
Four tools are appropriate for a specialized genomic data server. Schema is a mandatory prerequisite, query enables flexible exploration, gene_phenotype_detail addresses the server's primary analysis use case, and variants provides deeper variant-level data. The count is compact and focused without being insufficient.
The server covers the main workflows: understanding the schema, running analytical SQL queries, performing replication checks, and accessing variant-level results. It lacks explicit tools for listing available traits or genes, but these can be obtained via query. The set is functionally complete for its domain, with minor gaps.
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