ReddRadar
Agent skill
deepvariant-caller
DeepVariant deep learning variant calling skill for high-accuracy SNV and indel detection
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/deepvariant-caller
Metadata
Additional technical details for this skill
- tags
-
variant-analysis deep-learning snv indel
- version
- 1.0
- category
- bioinformatics
SKILL.md
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)
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