Jean — Molecular Biology & Genomics

apply_variant_call

Read-only

Substitute one called ALT allele into a sequence and return the edited bases, the range the edit occupies and the length change.

Input Schema

Name	Required	Description
`pos`	Yes	the POS of the record to apply, 1-based as VCF writes it.
`file`	No	which call set the variant comes from, by name. Unset, it is the project's only one.
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`contig`	Yes	the contig of the record to apply, as the file names it.
`offset`	No	the coordinate this sequence's FIRST base has in the call set's contig. Default 1, meaning the sequence starts at the contig's start. A plasmid extracted from a genome sets this to where it was cut from, which is what lets a genomic call be applied to it at all.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`sequence`	Yes	the sequence to edit.
`alt_index`	No	which ALT of a multiallelic record to apply, counting from 1 as the file lists them. Default the first.

Output Schema

Name	Required	Description
`delta`	Yes	signed length change, which is what any annotation downstream of the edit must shift by
`applied`	Yes	the record as applied: chrom, pos, ref, the ALT chosen and its index, so a run record says which allele of a multiallelic site was taken
`summary`	Yes	the edit in one sentence, generated from this run
`sequence`	Yes	the sequence with this ALT substituted for the REF, ready to wire into a next step. Every base outside the edited range is unchanged, and the length differs from the input by `delta`, so any coordinate downstream of `edited_start` has moved by that much
`edited_end`	Yes	0-based INCLUSIVE end of the edited range in the new sequence. Inclusive, not half-open, because it is the end of a selection a reader is meant to see highlighted rather than a slice bound
`edited_start`	Yes	0-based inclusive start of the range the edit occupies in the NEW sequence, for selecting it

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

B3.3/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the agent knows this is a safe, non-mutating computation. The description adds the shape of the result (edited bases, occupied range, length change), but doesn't state that the input sequence is left unchanged, nor how multiallelic or out-of-range positions are handled.

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

Conciseness5/5

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

A single front-loaded sentence with zero filler: the action comes first and the return payload follows. Nothing in it is redundant.

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

Completeness3/5

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

The tool has eight parameters including nested _subject and _files objects, but an output schema exists and schema coverage is complete, so the description needn't explain return values or individual parameters. It still omits any workflow context — how a call is selected from a file and what happens when the record doesn't match the sequence.

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

Parameters3/5

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

Schema description coverage is 100%, so pos, contig, sequence, file, offset and alt_index are all documented in the schema, including the subtle coordinate-offset behavior. The description adds no meaning beyond that, so the baseline of 3 applies.

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

Purpose4/5

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

States a specific verb and resource ("Substitute one called ALT allele into a sequence") and even previews the return (edited bases, edit range, length change). An agent can tell this applies an existing call rather than predicting effects like variant_consequences, but no sibling is named explicitly.

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

Usage Guidelines2/5

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

There is no when-to-use or when-not-to-use guidance, no mention of prerequisites such as first obtaining calls via read_variant_calls, and no pointer to alternatives for effect prediction or multi-variant application. Usage must be inferred entirely from the name and description.

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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