alphagenome_predictor
Predict regulatory effects of genetic variants on gene expression, chromatin accessibility, splicing, and promoter activity using AlphaGenome. Requires API key and pre-analysis planning with 'think' tool.
Instructions
Predict variant effects on gene regulation using Google DeepMind's AlphaGenome.
Input Schema
Name | Required | Description | Default |
---|---|---|---|
alternate | Yes | Alternate allele(s) (e.g., 'T', 'A') | |
api_key | No | AlphaGenome API key. Check if user mentioned 'my AlphaGenome API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one. | |
chromosome | Yes | Chromosome (e.g., 'chr7', 'chrX') | |
interval_size | No | Size of genomic interval to analyze in bp (max 1,000,000) | |
position | Yes | 1-based genomic position of the variant | |
reference | Yes | Reference allele(s) (e.g., 'A', 'ATG') | |
significance_threshold | No | Threshold for significant log2 fold changes (default: 0.5) | |
tissue_types | No | UBERON ontology terms for tissue-specific predictions (e.g., 'UBERON:0002367' for external ear) |