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Deepvariant caller

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/deepvariant-caller

DeepVariant deep learning variant calling skill for high-accuracy SNV and indel detectionFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill deepvariant-caller

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.5 KB, 175 tokens by cl100k_base, as published. Nobody here has run it

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)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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