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deepvariant-caller

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DeepVariant deep learning variant calling skill for high-accuracy SNV and indel detection

QUICK START

How to use this skill

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  1. Open your project in Codex.
  2. Copy the prompt below and paste it into your agent.
  3. Review the proposed files and risks before you approve installation.
Prompt to paste
I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/deepvariant-caller/SKILL.md

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First, summarize what it does, its dependencies, license status if identifiable, and any risks. Show the exact files you propose to add under .agents/skills/deepvariant-caller/. Do not write files or run scripts until I approve.

After I approve, install the complete skill folder, including required referenced files, into that project location. Verify it is discoverable, then tell me its actual invocation name and how to use it. Do not claim it is installed until you have verified it.

Copying this prompt does not install or run the skill. Review third-party files before use. Codex skill guide

DeepVariant Caller Skill

Purpose

Enable DeepVariant deep learning variant calling for high-accuracy SNV and indel detection.

Capabilities

  • GPU-accelerated variant calling
  • WGS/WES/PacBio mode selection
  • Model customization and retraining
  • Confidence calibration
  • Multi-sample variant calling
  • Docker/Singularity deployment

Usage Guidelines

  • Select appropriate model for sequencing type
  • Use GPU acceleration when available
  • Validate accuracy against benchmark datasets
  • Consider container deployment for reproducibility
  • Document model version and parameters
  • Compare with traditional callers for validation

Dependencies

  • DeepVariant
  • Parabricks

Process Integration

  • Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)
  • Long-Read Sequencing Analysis (long-read-analysis)
  • Analysis Pipeline Validation (pipeline-validation)