What problem does it solve? Prioritizing which genetic variants are functionally important from large callsets is slow and requires integrating many genomic data modalities. This Skill scores, annotates, and ranks variants using AlphaGenome Variant Impact (AVI) models through the AlphaGenome Atlas API, returning calibrated Phred scores and biological feature attributions. ## Core Features & Use Cases - Variant Querying & Scoring: Query single or multiple variants in chr:pos:ref>alt format to get AVI Phred scores, quantiles, and 18 biological feature attribution weights. - VCF/Tabular Annotation: Annotate VCF, CSV, TSV, or Parquet callsets in Ensembl VEP CSQ format and rank top candidate variants. - Saturation Mutagenesis Scans: Score all possible single-nucleotide substitutions across a genomic window to find functional hotspots. - GENCODE v46 Gene Annotations: Extract exon, CDS, UTR, and splice junction coordinates for genes and transcripts. - Use Case: Given a VCF of 1,000 rare variants from a sequencing study, annotate each with AVI scores, filter to Phred >= 20 (top 1% genome-wide), and identify the top splicing-disrupting candidates with Atlas deep-links. ## Quick Start Ask the assistant to score the variant chr9:128225994:G>A with the AlphaGenome AVI skill and show its Phred score and top contributing biological modality.
