MCP App StoreMCP App StoreThis skill ingests a structural-variant VCF (from callers like Manta, Delly, Sniffles) and produces a CSV table and report summarising each variant with SVTYPE, absolute SVLEN, and a size class. It aggregates per-type counts (DEL/DUP/INV/TRA/INS) and provides a machine-readable result.json plus a human report.md for quick review. The skill includes a demo mode to generate synthetic SV VCFs for testing.
Use this skill when you already have an SV VCF and need a compact summary or table for downstream analysis, QC, or reporting. Do NOT use it for calling SVs from BAMs — run an SV caller upstream (Manta/Delly/Sniffles) first. Good for pipeline smoke tests, QC dashboards, and feeding annotation steps.
references/ docs describing parameters, methodology, and output contract--input required unless --demo; --n-svs controls demo size. Notes document gotchas (BND records, SVLEN sign handling, demo limitations).Agents or CLIs that orchestrate bioinformatics pipelines (CLI-focused agents, workflow runners, or research assistants with shell/CLI access). This skill is best used by agents that can run Python CLIs and manage files (e.g., Codex/Copilot-style automation or custom pipeline orchestrators).
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