# Deepvariant Caller

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

- Skill: `a5c-ai/deepvariant-caller` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/deepvariant-caller`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/deepvariant-caller/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/deepvariant-caller

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# 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)