Jean — Molecular Biology & Genomics

copy_number_allele_split

Read-only

Read an Affymetrix array result's own allele-specific copy number: for each segment the major and minor allele counts (1+1, 2+0, 0+0), what they mean (balanced, allelic imbalance, loss of heterozygosity placed against the sample's own ploidy, homozygous deletion), and ASCAT's whole-genome summary over them (LOH fraction, homozygous deletions, modal allele state, whole-genome doubling, genomic instability).

Input Schema

Name	Required	Description
`file`	No	which copy-number file in this project, by name. Unset, it is the project's only one, and it refuses rather than guessing when there are several.
`_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.
`estimated_only`	No	report only the segments the producer split. Default false: an unestimated segment is listed as such, which is a different answer from its absence.

Output Schema

Name	Required	Description
`metrics`	Yes	ASCAT 3.2.0's ascat.metrics() profile columns over the estimated segments, unrounded: n_segs, segs_size, size_odd_segments, size_intermediate_segments, homdel_segs, homdel_largest, homdel_size, homdel_fraction, LOH (autosomal fraction), mode_minA, mode_majA, WGD (0, 1, '1+' or null) and GI (null when WGD is). Null when nothing is estimated
`summary`	Yes	how many segments carry a split, how many are LOH (and copy-neutral), homozygous deletions, imbalanced and balanced, and the autosomal LOH fraction
`segments`	Yes	one entry per segment: chromosome (the file's own name, X not 24), start and end (the file's coordinates), markers, estimated, major and minor (null where not estimated), raw_a and raw_b (the producer's raw nA/nB, null where empty), total_cn (the producer's total, fractional where it made no integer call), state (not-estimated, homozygous-deletion, loh, balanced, imbalanced) and relative_to_ploidy (below, equal, above, for LOH only, null when no ploidy is stated)
`provenance`	Yes	which file answered, the data set the split was read from, how many segments it holds and how many are estimated, and the producer's own fit: ploidy and aberrant-cell fraction as the chip summary states them

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.5/5.0

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 the safety profile is covered. The description adds useful behavioral context by explaining the per-segment allele counts, their interpretations, and the ASCAT whole-genome summary. It does not mention limitations such as file-selection behavior, but the schema covers that.

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?

The description is a single, front-loaded sentence that begins with the verb and resource. It is dense but well-structured, using parenthetical examples to clarify allele states and summary metrics. It could be slightly more concise, but every clause contributes useful information.

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?

The tool has an output schema and annotations, so the description need not explain return values in full. It nevertheless describes the key outputs and their interpretation, which is helpful. The main gap is the absence of usage guidance relative to sibling copy-number tools, but the core purpose and behavior are complete.

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 the input schema already documents all four parameters in detail. The description does not add meaning beyond the schema for parameters like file, _files, _subject, or estimated_only. A baseline score of 3 is appropriate when the schema does the heavy lifting.

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?

The description states a specific verb and resource: reading an Affymetrix array result's allele-specific copy number. It details the per-segment major/minor allele counts and ASCAT summary, making the tool's purpose clear. It does not explicitly distinguish itself from sibling tools such as copy_number_loh or copy_number_segment, so it falls short of a 5.

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?

The description gives no explicit guidance on when to use this tool versus alternatives. It implies usage by describing what is read, but does not state when-not to use it or name sibling tools that might be more appropriate. This leaves the agent to infer selection from the name and description alone.

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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