Variant Calling (GATK4) — Pipeline Skill (Thin Scaffold)

Overview

Adds decision logic for VQSR vs hard filters, WES vs WGS parameter differences, and GATK4-specific gotchas that LLMs frequently get wrong (filter thresholds, GVCF requirements, reference consistency).

Usage

• Activate when choosing between VQSR and hard filters for a given cohort size
• Activate when setting up WES vs WGS pipeline parameters
• Activate when running Mutect2 tumor/normal or tumor-only somatic calling

Core Concepts

Decision Logic