Performs data cleaning and removal operations. This skill takes a raw BAM and creates a new, "clean" BAM file by actively removing artifacts: mitochondrial reads, blacklisted regions, PCR duplicates, and unmapped reads. Use this skill to "clean," "filter," or "remove bad reads" from a dataset. This is a prerequisite step before peak calling. Do NOT use this skill if you only want to view statistics without modifying the file.
6.1
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Data & Analytics
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Excellent bioinformatics skill for BAM file filtration with clear, actionable documentation. The description precisely defines when to use/not use the skill, making it highly suitable for CLI agent invocation. Task knowledge is comprehensive with specific tool calls, parameters, and a logical decision tree. Structure is clean and well-organized with clear sections for inputs, outputs, and workflow steps. The skill addresses a real bioinformatics need (removing artifacts before peak calling) that would otherwise require multiple manual tool invocations and domain expertise. Minor points: the skill could benefit from error handling guidance and the novelty is moderate since it wraps existing bioinformatics tools in a structured way, though it does meaningfully simplify a multi-step process that requires domain knowledge about blacklists, PCR duplicates, and proper filtering order.
majiayu000
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