deepvariant-caller

# 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)