tooluniverse-variant-analysis
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions. Parses VCF files (streaming, large files), classifies mutation types (missense, nonsense, synonymous, frameshift, splice, intronic, intergenic) and structural variants (deletions, duplications, inversions, translocations), applies VAF/depth/quality/consequence filters, annotates with ClinVar/dbSNP/gnomAD/CADD via ToolUniverse, interprets SV/CNV clinical significance using ClinGen dosage sensitivity scores, computes variant statistics, and generate
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-variant-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Variant Analysis and Annotation Production-ready VCF processing and variant annotation skill combining local bioinformatics computation with ToolUniverse database integration. Designed to answer bioinformatics analysis questions about VCF data, mutation classification, variant filtering, and clinical annotation. ## When to Use This Skill **Triggers**: - User provides a VCF file (SNV/indel or SV) and asks questions about its contents - Questions about variant allele frequency (VAF) filtering - Mutation type classification queries (missense, nonsense, synonymous, etc.) - Structural variant interpretation requests (deletions, duplications, CNVs) - Variant annotation requests (ClinVar, gnomAD, CADD, dbSNP) - CNV pathogenicity assessment using ClinGen dosage sensitivity - Cohort comparison questions - Population frequency filtering (SNVs or SVs) - Intronic/intergenic variant filtering - Gene dosage sensitivity queries **Example Questions**: - "What fraction of variants with VAF < 0.3 are annotated as missense mutations?" - "After filtering intronic/intergenic variants, how many non-reference variants remain?" - "What is the clinical significance of this deletion affecting BRCA1?" - "W
- When to Use This Skill
- Core Capabilities
- Workflow Overview
- Phase Summaries
- Phase 1: VCF Parsing
- Phase 2: Variant Classification
- Phase 3: Filtering
- Phase 4: Statistics
- Phase 5: ToolUniverse Annotation
- Phase 6: Report Generation
- Phase 7: Structural Variant & CNV Analysis
- Answering BixBench Questions
- Pattern 1: VAF + Mutation Type Fraction
- Pattern 2: Cohort Comparison
What does the tooluniverse-variant-analysis skill do?
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions. Parses VCF files (streaming, large files), classifies mutation types (missense, nonsense, synonymous, frameshift, splice, intronic, intergenic) and structural variants (deletions, duplications, inversions, translocations), applies VAF/depth/quality/consequence filters, annotates with ClinVar/dbSNP/gnomAD/CADD via ToolUniverse, interprets SV/CNV clinical significance using ClinGen dosage sensitivity scores, computes variant statistics, and generate
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-variant-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.