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