gatk-variant-calling
CommunityCall SNPs & indels with GATK Best Practices.
Authorjaechang-hits
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill automates the complex process of identifying genetic variations (SNPs and indels) in DNA sequencing data, a crucial step for research and clinical diagnostics.
Core Features & Use Cases
- Germline Variant Calling: Implements the GATK Best Practices pipeline for accurate SNP and indel detection from WGS/WES data.
- Cohort Analysis: Supports joint genotyping across multiple samples for comprehensive population studies.
- Data Quality Improvement: Includes Base Quality Score Recalibration (BQSR) to enhance variant calling accuracy.
- Use Case: Analyze whole-genome sequencing data from a cohort of cancer patients to identify somatic mutations associated with disease progression.
Quick Start
Run the GATK Best Practices pipeline for germline variant calling on your aligned BAM files.
Dependency Matrix
Required Modules
gatk4samtoolsbcftoolsbwa-mem2java
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: gatk-variant-calling Download link: https://github.com/jaechang-hits/SciAgent-Skills/archive/main.zip#gatk-variant-calling Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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