skills/bioskills/bio-clinical-databases-acmg-classification/scripts/acmg_classify.py

• pejaver_calibrate · function · L51-L58 — def pejaver_calibrate(score, thresholds)
• revel_pp3_bp4 · function · L61-L63 — def revel_pp3_bp4(revel_score)
• bayesdel_pp3_bp4 · function · L66-L68 — def bayesdel_pp3_bp4(bayesdel_noaf_score)
• spliceai_walker2023 · function · L71-L85 — def spliceai_walker2023(ds_max)
• alphamissense_supporting_only · function · L88-L101 — def alphamissense_supporting_only(am_score)
• pvs1_decision_tree · function · L104-L135 — def pvs1_decision_tree(variant_type, is_in_5prime_or_pre_last_exon_junction, coding_pct_removed, in_critical_region, is_alt_isoform_in_disease_tissue=True)
• whiffin_max_credible_af · function · L138-L144 — def whiffin_max_credible_af(prevalence, max_allelic_contribution=1.0, max_genetic_contribution=1.0, penetrance=1.0)
• bs1_ba1 · function · L147-L160 — def bs1_ba1(grpmax_faf95, max_credible_af, ba1_threshold=0.05)
• ps3_oddspath · function · L163-L188 — def ps3_oddspath(odds_path)
• tavtigian_classify · function · L191-L207 — def tavtigian_classify(criteria_assigned)
• classify_with_subsumption · function · L210-L221 — def classify_with_subsumption(criteria_assigned)
• genebe_api · function · L224-L233 — def genebe_api(hgvs)
• cancer_amp_tier · function · L237-L255 — def cancer_amp_tier(biomarker_in_oncokb_level, in_nccn_guidelines=False, same_tumor_type=False, evidence_quality='preclinical')