What problem does it solve? Manually constructing AlphaGenome Atlas URLs is error-prone: variant formats must be 1-based chr:pos:ref>alt, filter groups follow non-obvious AND/OR logic, and track-prediction ScoreId tokens require exact splice junction coordinates, strand rules, and track catalog names. This Skill automates correct URL synthesis for variants, loci, candidate tables, and Ref vs. Alt comparisons. ## Core Features & Use Cases - Variant & Locus Deep-Links: Build single-variant exploration links and genomic interval views with biosample, modality, and transcription factor filters, automatically enforcing the Assay-group rule so RNA-seq and DNase tracks stay visible. - Candidate Summary Tables: Format ranked variant records into Markdown tables with embedded clickable Atlas links. - Track Predictions (Ref vs. Alt): Generate /atlas/track-predictions URLs that resolve GENCODE v46 splice junctions, query the Atlas track catalog, and co-plot RNA-seq with splicing tracks. - Use Case: Given a splice variant like chr15:42387805:C>G in CAPN3, produce a bounded track-predictions link comparing reference and alternate allele predictions across splice junctions, RNA-seq, DNase, and ChIP-TF in Muscle_Skeletal. ## Quick Start Ask the assistant to generate an AlphaGenome Atlas deep-link for the variant chr9:128225994:G>A in K562 cells with RNA-seq, DNase, and ChIP-TF tracks.
