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Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller. Distinguishes de novo CALLING (scanning a panel for unknown variants, bounded by per-locus error and multiple testing) from tumor-informed DETECTION (tracking a pre-specified variant set, where panel integration reaches single-ppm). Covers VarDict and Mutect2 for de novo calling, UMI-aware callers, and a pysam-based known-variant VAF tracker, with matched-WBC subtraction as the mandatory defense against clonal hematopoiesis (the dominant false positive). Use when calling or tracking tumor mutations from plasma cfDNA, setting a VAF threshold, or deciding whether a low-VAF call is tumor versus CHIP.

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Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.

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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.

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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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This skill suggests targeted therapies (somatostatin analogs or tyrosine kinase inhibitors) to treat ectopic ACTH syndrome when ectopic ACTH secretion is confirmed or strongly suspected. Use when triggers include occult or metastatic ectopic ACTH secretion, very severe ACTH‑dependent disease uncontrolled by medical therapy, or when surgery is not possible or noncurative.

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Monitors glucocorticoid replacement in primary adrenal insufficiency (PAI) patients using clinical assessment of body weight, postural blood pressure, energy levels, and signs of frank glucocorticoid excess. Trigger phrases include "PAI patient on glucocorticoid replacement," "assess for weight gain or insomnia," and "evaluate for postural hypotension or fatigue."

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Look up NHS England genomic tests for rare and inherited diseases. Use this skill whenever a clinician asks what genetic test to order for a condition, which genes are covered for a specific diagnosis, what commissioning category a genomic test falls under (Core, Specialised, or Highly Specialised), or which tests belong to a specialty group (Neurology, Cardiology, Endocrinology, etc.). Also trigger for questions like what panel is used for a condition, whether there is an NHS test for something, what the R number is for a condition, or whether anything has changed in the genomic test directory. Source: NHS England National Genomic Test Directory for Rare and Inherited Disease v9.0 (April 2026).

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This skill guides annual evaluation of patients with primary adrenal insufficiency (PAI) for symptoms and signs of glucocorticoid and mineralocorticoid over- or under-replacement. Use during annual follow-up when assessing for weight changes, blood pressure abnormalities, edema, or symptoms such as fatigue, insomnia, or salt craving.

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Capture what someone actually said without contaminating it with your own inference. Invoke when eliciting intent in conversation (design discussion, requirement interview, decision surfacing) and when turning a conversation into a durable record (ADR, decision node, memory entry, spec `## Decisions` row). Enforces quote-before-critique, keeps illustration separate from commitment, and holds interpretation subordinate to verbatim. Prevents the failure where unspecified space is filled by the recorder and then evaluated as if the speaker had specified it.

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When the user wants to write, rewrite, or improve marketing copy for any page — including homepage, landing pages, pricing pages, feature pages, about pages, or product pages. Also use when the user says "write copy for," "improve this copy," "rewrite this page," "marketing copy," "headline help," "CTA copy," "value proposition," "tagline," "subheadline," "hero section copy," "above the fold," "this copy is weak," "make this more compelling," or "help me describe my product." Use this whenever someone is working on website text that needs to persuade or convert. For email copy, see email-sequence. For popup copy, see popup-cro. For editing existing copy, see copy-editing.

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Take a markdown file of raw material and shape it into an article through a conversational session — drafting candidate openings, growing the piece paragraph by paragraph, arguing about format (lists, tables, callouts, quotes) at each step. Use when the user has a pile of notes, fragments, or a rough draft and wants help turning it into something publishable.

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Disciplined diagnosis loop for hard bugs and performance regressions. Reproduce → minimise → hypothesise → instrument → fix → regression-test. Use when user says "diagnose this" / "debug this", reports a bug, says something is broken/throwing/failing, or describes a performance regression.

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Marc Andreessen-mode decision and productivity skill. A blunt, market-first operator that pressure-tests ideas, ventures, features, and career bets through Andreessen's actual frameworks — market dominates team and product; the only milestone that matters is product/market fit; bias to build over deliberate. Use when the user says 'andreessen', 'pmarca mode', 'should I build this', 'is there a market', 'are we at product/market fit', 'pmf check', 'pressure-test this idea', 'be brutal about this venture', 'market-first take', or wants a no-disclaimers, no-hedging, confidence-leveled verdict on whether something is worth pursuing. Also provides the 3x5-card + Anti-Todo personal productivity routine. Runs on a fixed anti-sycophancy operating prompt: leads with the strongest counterargument, never validates premises, uses explicit confidence levels, never apologizes for disagreeing. Not for polite brainstorming — this skill exists to tell you the market is dead when it is.

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Verify every claim from multiple independent angles -- code, docs, tests, git history. Use when you need high confidence that something is correct before acting on it.

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Verify like Fable 5 — obsessive, systematic, evidence-based quality assurance woven into your reasoning. Use this skill when you have just written or modified code, need to confirm something works, are running tests, or need to validate output against requirements.

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Learns a user's personal writing and speaking style through interactive writing prompts, then generates a reusable voice profile. Use when the user says "learn my writing style," "write like me," "capture my voice," "voice calibration," "mimic my tone," "my writing style," or wants AI to match their personal communication style. Also activates when a .voice-profile.md file exists and the user asks you to write something in their voice.

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Splits scarce time, budget or traffic across competing products, channels, campaigns or variants by treating them as a multi-armed bandit - Thompson sampling over beta posteriors, with optimism for anything not yet tried enough to judge. Use when deciding what to work on next, how to divide a marketing budget, which product to prioritise, whether to kill something that is underperforming, or when picking a winner among test variants.

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Separates signal from noise in metrics you cannot observe directly, updating a belief from evidence instead of reacting to the latest reading - Bayesian updates over competing explanations, and a filter that says whether this week's move is real. Use when a metric moves and someone wants to act, when diagnosing why traffic or revenue changed, when a dashboard number contradicts intuition, or when deciding whether a trend is real yet.

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Turns a vague "what should we do about X" into a scored decision - explicit actions, an explicit unknown, an explicit prior, and one utility scale - then picks by maximum expected utility and checks the result for framing effects. Use when facing a choice between options under uncertainty, when a decision has stalled in circular debate, when someone asks "should we do A or B", or before writing any decision record, strategy memo, or roadmap commitment.

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Prices research, tests, surveys, dashboards and experiments before running them, by computing how much the result would raise expected utility - which is zero whenever no outcome would change the decision. Use when someone proposes an A/B test, user survey, market study, competitor analysis, analytics build, consultant, pilot, or "let's gather more data", and when deciding how large a study needs to be.

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Generates premium, multi-page, mobile-optimized (1:1 aspect ratio) PDF marketing brochures for exclusive retreats, workshops, luxury events, or any high-end product/service offering. Use this skill whenever a user asks to create a brochure, marketing PDF, event flyer, WhatsApp marketing material, social media brochure, or design a multi-page promotion document. Also trigger when users mention wanting to promote an experience, product, or service and need visual marketing material. Even if the user just says "make a brochure for my event" or "I need a PDF for my product," use this skill.

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