Maftools-MCP：基于 Model Context Protocol 的 LLM 驱动体细胞突变分析框架
Maftools-MCP: A Model Context Protocol–enabled Framework for LLM–driven Somatic Mutation Analysis
Maftools-MCP 是一个基于 Model Context Protocol 的框架，可将自然语言请求转换为结构化的工具调用，从而驱动基于 R 的 Maftools 完成体细胞突变分析。该框架还配套开发了一个 agent skill，用于在下游 Maftools 分析前完成上游变异注释。评估涵盖逐工具验证、在 5 个语言模型（含商业模型与本地部署模型）上重复执行 3 个代表性用例，以及将集成注释流程与直接执行的参考流程进行对比。Maftools-MCP 已在公开地址提供。
来源：Bioinformatics Advances · doi.org
Motivation
Somatic mutation analysis is routine in cancer genomics, but the scale and complexity of next-generation sequencing data can make analysis challenging. Maftools is widely used for somatic variant analysis and visualization, yet its R-based workflow can be difficult for non-programmers, while graphical interfaces may provide access to only predefined analytical options.
Results
We developed Maftools-MCP, a framework based on the Model Context Protocol that translates natural-language requests into structured tool calls for Maftools analysis. Maftools-MCP demonstrates how this protocol can enable natural-language interaction with an R-based analytical package while allowing flexible control of exposed functions and parameters. We also developed an agent skill to support upstream variant annotation before downstream Maftools analysis. Evaluation included per-tool validation, repeated execution of three representative use cases across five language models, including commercial and locally deployed models, and comparison of an integrated annotation workflow with a directly executed reference workflow.
Availability and implementation
Maftools-MCP is publicly available at http://tardis.cgu.edu.tw/maftools-mcp.