workbench

Variant Annotator

variant_annotate

Read-onlyIdempotent

One-box variant lookup against MyVariant.info: accepts an rsID, chrom:pos:ref:alt, genomic HGVS ("chr17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G" / "TP53:c.215C>G", bridged via the hgvs_convert tool). Returns a ClinVar significance summary, gnomAD exome/genome allele frequencies, and CADD/SIFT/PolyPhen2/REVEL pathogenicity predictor scores — each section explicitly null when that source has no data, never silently omitted. See the result's own "caveats" for real data-freshness limits (frozen gnomAD/CADD snapshots, periodic ClinVar snapshot).

Input Schema

TableJSON Schema

Name	Required	Description	Default
`variant`	Yes	An rsID ("rs1042522"), chrom:pos:ref:alt ("17:7676154:G:C", single-base substitutions only), genomic HGVS ("chr17:g.7676154G>C" or "17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G" or "TP53:c.215C>G").
`assembly`	No	Genome build for rsID/chrom-pos-ref-alt/genomic-HGVS lookups (MyVariant.info's native default is hg19). Ignored for transcript "c." input, which is always bridged via GRCh38/hg38 (hgvs_convert's own coordinate space).	hg19

TDQS

A4.3/5.0

Behavior4/5

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

Annotations already declare readOnlyHint=true and idempotentHint=true. The description adds that missing data is explicitly null (never silently omitted) and directs users to a 'caveats' section for data freshness. No contradiction with annotations.

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?

Single paragraph with logical flow: purpose, input formats, output content, and data handling. No redundant sentences, but could be slightly more streamlined by separating input and output into bullet points. Still very efficient.

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

Completeness4/5

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

Given no output schema, the description covers key results (fields returned) and behavior (null handling, caveats). It is sufficient for a read-only lookup tool. Lacks specification of pagination or limits, but these are likely unnecessary.

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% with descriptions for both parameters. The description enhances the 'variant' parameter by enumerating all accepted formats with examples and clarifies the assembly parameter's behavior depending on input type. This adds meaningful context beyond the 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?

Clearly states it is a variant lookup tool returning annotations from MyVariant.info. Lists all accepted input formats (rsID, chrom:pos:ref:alt, genomic HGVS, transcript HGVS) and output content (ClinVar, gnomAD, pathogenicity scores). Distinguishes itself from sibling tools like hgvs_convert and variant_comparator through explicit input format handling and output scope.

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?

Provides clear context that this is a single-variant lookup tool and mentions the need to use hgvs_convert for transcript HGVS inputs. However, it does not explicitly state when to avoid this tool or mention alternatives for comparing variants, though sibling names imply differentiation.

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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TDQS

A3.6/5.0

Disambiguation4/5

Most tools have highly specific purposes (e.g., crispr_grna_design vs base_editing_design vs prime_editing_design). However, there is some overlap in sequence analysis tools (characterize_sequence, sequence_report) and plasmid annotation tools (plasmid_annotate vs plasmid_deep_annotate) which could cause confusion.

Naming Consistency3/5

The naming pattern is largely consistent with snake_case verb_noun or noun_descriptor (e.g., primer_design, plasmid_annotate, fastq_trim). However, there are exceptions like 'batch', 'workflow', 'gc_content', and 'cloning_diagnose' which don't follow the verb_noun pattern consistently. Also, some names are phrases like 'golden_gate_from_parts'.

Tool Count2/5

With 101 tools, this server is extremely large and likely overwhelming for agents. Even for a comprehensive bioinformatics toolkit, this exceeds a manageable scope, risking agent confusion and inefficient tool selection. A more modular approach would be advisable.

Completeness4/5

The tool surface covers a wide range of bioinformatics workflows including sequence analysis, primer design, cloning, CRISPR, NGS, expression analysis, and data export. There are minor gaps such as lack of a dedicated protein structure prediction tool and limited off-target genome coverage, but overall the set is impressively complete for its domain.

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