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 and strand rules. This Skill automates correct URL generation for variants, loci, candidate tables, and Ref vs. Alt prediction 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. - Candidate Variant Tables: Format ranked variant records into Markdown tables with embedded clickable Atlas links. - Track Predictions: Generate /atlas/track-predictions URLs comparing Reference vs. Alternate allele predictions, with automatic GENCODE v46 splice junction resolution and mandatory RNA-seq co-plotting. - Use Case: Given a splicing variant like chr15:42387805:C>G in CAPN3, produce a bounded track-predictions link showing splice junctions, RNA-seq, DNase, and ChIP-TF tracks in Muscle_Skeletal tissue. ## 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.
