jean — Molecular Biology & Genomics

detect_trace_indel

Read-only

Ask whether a Sanger trace splits into TWO READS OF DIFFERENT LENGTH, which is what a heterozygous insertion or deletion does: clean up to the indel, then a superposition of two sequences offset by its length. This is not mixed-base calling — that asks whether two BASES sit at one position and is blind to a length difference. Emits where the split starts, how long it is, and the two allele sequences the trace deconvolves into, so a pipeline can gate on the answer or carry either allele onward.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`table`	No	the instrument and polymer the quality scale was calibrated on. There is no universal default: a base scores differently under a different table, and the detector gates on a quality JUMP.	3730pop7
`_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.
`_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.
`document`	No	which trace file to read: its name (`read_F.ab1`) or its project file id. LEAVE IT EMPTY to run on the chromatogram tab that is open, in which case the answer also appears in the rail. A file id is project-specific, so a template ships this unset.
`breakpoint_scan`	No	skip the search and measure the indel at this scan position on the x axis. -1 searches for it.
`quality_value_reading`	No	corrected = read the quality values as TraceTuner's own header declares them, which is the only reading that can detect anything; upstream = reproduce the program as shipped, whose detector never fires.	corrected

Output Schema

TableJSON Schema

Name	Required	Description
`found`	Yes	whether a heterozygous indel was detected. Wire it into a gate
`report`	Yes	the whole finding, including the size in scans and the stutter verdict
`longAllele`	Yes	the allele with the extra bases, from the breakpoint on. N marks a position the deconvolution would not commit to, not a low-quality base
`qualityJump`	Yes	the drop in quality values across the breakpoint. It must exceed 7 for a position to be considered at all, so this is what a negative answer is checkable against
`shortAllele`	Yes	the allele without them, from the breakpoint on
`sizeInBases`	Yes	how many bases the longer allele carries that the shorter one does not
`startsAtBase`	Yes	the 1-based base the split starts at, or 0 when none was found

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.1/5.0

Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so safety is covered. The description adds real behavioral context beyond that: the deconvolution model (clean read up to the indel, then two offset sequences) and what it emits, which helps the agent interpret a positive call.

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 core question, then the biological mechanism, then the contrast with mixed-base calling, then the emission. Dense but every sentence carries signal; the contrast clause is arguably the only non-essential part.

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?

With an output schema describing the emitted breakpoint, length and allele sequences, and full annotation coverage, the description need not explain return values. It supplies purpose, mechanism and disambiguation, leaving only fine-grained parameter guidance to the schema.

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 every parameter (table, document, breakpoint_scan, quality_value_reading, _subject, _files) is already documented in the schema. The description adds nothing about parameter behavior, so the baseline 3 applies.

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 precise, specific question ('does the trace split into TWO READS OF DIFFERENT LENGTH') and the biological cause (heterozygous indel), and explicitly distinguishes itself from mixed-base calling. An agent can tell it apart from call_mixed_bases_from_trace without opening either schema.

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 a clear condition for selection (heterozygous insertion/deletion lookahead) and rules out the nearest alternative ('This is not mixed-base calling'), plus notes the result can gate a pipeline or carry an allele onward. It does not name the exact sibling tool, leaving a small inference gap.

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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