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Scored across 24 tools
Several tools return essentially the same 'strongest effect per modality' summary — predict_variant_effect, assess_pathogenicity, annotate_regulatory_context, generate_variant_report and explain_variant_impact overlap heavily, differing mainly in verbosity. The comparison family (compare_variants, compare_alleles, compare_variants_same_gene, compare_protective_risk, batch_tissue_comparison) and the batch family (batch_score_variants, batch_modality_screen, batch_pathogenicity_filter, atlas_lookup_variants) also blur into each other. Legacy names that the descriptions explicitly disclaim (assess_pathogenicity, compare_protective_risk, batch_pathogenicity_filter) actively mislead selection.
All names are snake_case and almost all follow a verb_noun shape (predict_*, batch_*, compare_*, atlas_*, analyze_*, annotate_*, generate_*, explain_*). The atlas_* resource prefix and the varied verb set (predict/score/assess/analyze/compare/lookup/scan) are readable conventions rather than chaos. Minor deviation: some tools lead with an action while others lead with a scope prefix.
24 tools is on the heavy side for a variant-effect predictor, and a meaningful fraction are near-duplicates of a general scoring tool. Many could be folded into predict_variant_effect with parameters (modality, comparison mode, batch) without loss. The Atlas-vs-live distinction does justify some separate entries, but not this many.
The surface covers the full variant-scoring lifecycle: single variant, batch, region scan, Atlas lookup/list, per-modality breakdowns, tissue comparison, allele comparison and plain-language/narrative output. Gaps are minor — no non-variant sequence/annotation retrieval and no export/format options — but an agent can complete realistic prioritization workflows without dead ends.
