「variants」の検索結果

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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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.

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Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV and AnnotSV for semi-automated scoring. Covers the separate copy-number-loss and copy-number-gain rubrics, the five-tier classification, ClinGen haploinsufficiency/triplosensitivity and dosage-sensitive regions, de novo and segregation evidence, and population-frequency benign evidence. Use when assigning pathogenic/likely-pathogenic/VUS/likely-benign/benign to a constitutional CNV, scoring a CNV against ACMG/ClinGen criteria, or distinguishing the automatable evidence from the case-specific evidence requiring manual input.

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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).

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Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or long-range LD, or feeding credible sets into coloc.susie for colocalization.

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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.

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Unified skill for all MATLAB and Simulink report generation tasks. Covers report generation, PDF report, document generation, mlreportgen, Report Generator, template, TitlePage, Chapter, multipage HTML, HTMLPage, html-multipage, custom reporter, customizeReporter, template hole, page header, page border, company style package, branded reporters, buildTemplates, Simulink report, model documentation, slreportgen, block diagram report, model report, subsystem documentation, SystemDiagramFinder, SystemIO, ExecutionOrder, LookupTable, template style, page footer, TemplateSrc, report package, table variants, multiple HTML pages, PDF report generation, Word report, DOM API, FormalTable, BaseTable, Figure, FormalImage, Section.

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Customize Kubernetes manifests without templating using Kustomize. Create base configurations with environment overlays, manage configuration variants, and patch resources declaratively. Use when managing Kubernetes configurations across multiple environments without Helm.

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Create, amend, or backprop bugs into SPEC.md at repo root. Sole mutator of the project spec. Triggers when the user asks to write a spec, start a new spec, distill a spec from existing code, add invariants, amend sections (§G, §C, §I, §V, §T, §B), or record a bug via backprop. Common phrasings: "write the spec for...", "new spec", "bug: ...", "amend §V.3", "distill spec from code", "spec this idea". Reads and follows FORMAT.md for the caveman encoding rules and pipe-table shape of §T and §B.

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E-commerce email marketing system builder. Creates complete email automation flows with full copywriting, subject lines, ESP setup instructions, segmentation rules, and annual campaign calendars. Generates copy-paste-ready email sequences for Klaviyo, Omnisend, Mailchimp, or any ESP. Covers welcome series, cart abandonment, browse abandonment, post-purchase, review requests, cross-sell, win-back, VIP/loyalty, replenishment, and sunset flows. Includes A/B test subject line variants, send timing, trigger conditions, branching logic, and seasonal campaign calendar. No API key required. Use when: (1) setting up email marketing for an e-commerce store, (2) writing email sequences and flows, (3) planning seasonal email campaigns.

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Use when adding a new docs section or product area, editing llms.ts / the llms.txt or llms/[...slug] / llms-full.txt routes / get-llm-text / skill.md / .well-known endpoints, or working on the "agent score", "llms.txt", or anything "agent-ready" in the docs and site apps. Explains the invariants the Mintlify agent-readiness audit measures and how to hold them.

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Generate complete, accessible colour palettes from a single brand hex. Produces 11-shade scale (50-950), semantic tokens, dark mode variants, Tailwind v4 CSS output, WCAG contrast checks. Use whenever the user supplies a brand hex and asks for a palette, mentions setting up a design system, wants Tailwind theme colours from a brand colour, or asks to check colour accessibility / contrast.

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Create and manage Shopify products via the Admin GraphQL API or CSV import. Workflow: gather data, choose method, execute, verify. Use whenever the user wants to add products to Shopify, bulk-import a catalog from CSV/spreadsheet/URL, update variants or prices, manage inventory quantities, upload product images, or assign products to collections.

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Modern animation library for React and JavaScript. Create smooth, production-ready animations with motion components, variants, gestures (hover/tap/drag), layout animations, AnimatePresence exit animations, spring physics, and scroll-based effects. Use when building interactive UI components, micro-interactions, page transitions, or complex animation sequences.

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Use when a Unity 6.3 game is slow or stutters: low fps, frame spikes, hitches when entering areas or on first effects, GC spikes, too many draw calls or SetPass calls, CPU vs GPU bound questions, Profiler, Profile Analyzer, Memory Profiler, Frame Debugger or Project Auditor work, GPU Resident Drawer or SRP Batcher setup, LOD and Mesh LOD, shader warm-up and variants, memory or VRAM budgets, IL2CPP and build size, or proving a fix with numbers from a player.

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Use when generated clips must become a finished video on Scenario via MCP: cutting a shot list together, laying a timeline, concatenating with transitions, overlaying a logo or title card, adding a music bed or voiceover, burning in or exporting captions and subtitles, trimming and splitting, or producing vertical and square variants of one master. Keywords: edit, assemble, stitch, concat, compositor, timeline, layers, overlay, captions, SRT, ad, UGC, social cut.

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Use when producing a video ad with Scenario from a product shot or brand assets: a mobile 9:16 or landscape 16:9 commercial, a TikTok, Reels, Shorts, YouTube, or CTV spot, or campaign creative needing a creative brief, storyboard, cinematic camera work, brand-faithful product footage, music and voiceover, captions, ad variants, budget planning, or platform delivery specs. Keywords: video ad, commercial, product video, advert, hook, CTA, end card, campaign, ad creative.

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