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Use when predicting clinical pathogenicity of missense variants, scoring nonsynonymous SNVs for disease relevance, filtering rare variants by pathogenicity probability, annotating VCF files with ClinP
Use with AI
Install the MCP server or CLI to instantly fetch ClinPred documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/clinpred
GATK VQSR (Variant Quality Score Recalibration) — machine learning-based variant filtering for GATK Best Practices germline pipelines. Trains a Gaussian mixture model on truth/training resource datase
1 shared topic • 2 shared operations
VARITY -- machine-learning variant effect predictor for missense variants. Predicts pathogenicity of single amino acid substitutions using gradient boosting trained on ClinVar. Provides two models: VA
1 shared topic • 2 shared operations
Use when working with Borzoi — a sequence-to-function DNA foundation model — for predicting genome-wide regulatory activity from DNA sequences. Borzoi predicts RNA-seq, ATAC-seq, ChIP-seq, and histone
1 shared topic • 1 shared operation
DVC (Data Version Control) — Git-based version control for data, models, and ML experiments. Provides data versioning with .dvc files, ML pipeline definition via dvc.yaml DAGs, experiment tracking and
1 shared topic • 1 shared operation
Open Babel — open-source cheminformatics toolkit for chemical file format conversion, 3D coordinate generation, molecular fingerprint calculation, substructure and SMARTS pattern searching, descriptor
1 shared topic • 1 shared operation