Search: "variant"

Hunts for the other instances of a bug already found — the variants of one root cause across a codebase. Use immediately after a vulnerability, logic bug, or bad pattern turns up in a specific file and the question becomes where else it occurs, including the bare conversational form ("are there others like this?", "is this the same bug?"). Also for generalizing one known instance into a CodeQL or Semgrep query for its whole pattern family, and for triaging a set of look-alike candidates against a known root cause. Not for initial discovery with no bug in hand.

Expands one confirmed or suspected vulnerability into a Trailmark graph neighborhood of variant candidates by finding sibling functions, shared callers and callees, common sensitive sinks, common entrypoint paths, interface implementations, override relationships, type/reference neighbors, and structurally similar nodes. Use after one issue is found to seed variant-analysis, semgrep-rule-creator, static-analysis, or manual review with graph-derived candidate locations.

Validates security patches with reproducible baseline-versus-patched evidence, including original exploits, root-cause variants, behavior preservation, regressions, and newly introduced security failures. Use after a patch exists and before accepting, merging, or reporting it as fixed; also use when an AI-generated patch, remediation commit, pull request, or proposed upstream fix needs adversarial post-patch validation across any language.

Writes, reviews, and debugs property-based tests — Hypothesis, fast-check, proptest, jqwik, rapid, and Echidna or Medusa for Solidity invariants. Use whenever tests should cover a whole input domain instead of a hand-picked list of examples: encode/decode and serialize/deserialize pairs, parsers, canonicalizers and normalizers, validators, numeric and Decimal types, comparators and sort order, data structures, and smart-contract state invariants. Also use when adding cases to an existing @given, fast-check, or proptest suite, when judging whether existing property tests assert anything real, and when a generator has shrunk a counterexample and you need to tell a wrong property from a genuine bug. Not for coverage-guided binary fuzzing (libFuzzer, AFL), mutation-testing campaigns, static analysis, benchmarking, or end-to-end UI tests.

Creates language variants of existing Semgrep rules. Use when porting a Semgrep rule to specified target languages. Takes an existing rule and target languages as input, produces independent rule+test directories for each language.

Build and maintain a design system inside an Expo app - a reusable theme of design tokens (color, spacing, typography, radius, shadow, motion), reusable component structure with variant/size/state prop conventions, and rules for when to extract a repeated view into a shared component. Use when creating or organizing theme files and design tokens (theme.ts / theme/), extending an existing theme or styling library (NativeWind, Tamagui, Restyle, Unistyles) in its own idiom, standardizing styles so screens (including AI-generated ones) look consistent and polished, fixing an app that looks AI-generated or generic instead of native (the named native-slop tells), building an in-app component library, or auditing an app for design-system drift (hardcoded colors, spacing, fonts). For platform styling specifics (semantic colors, HIG rules, native controls) use expo-native-ui; for folder layout of a new app use expo-project-structure.

Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individuals. Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations.

Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export locally or through TileDB Cloud.

Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing, polyadenylation and contact-map tracks), scores variants or scans windows on demand with the AlphaGenome model for human and mouse (variant scoring, in silico mutagenesis, REF-versus-ALT track prediction), and builds Atlas website deep links. Use when the user mentions AlphaGenome, AlphaGenome Atlas, AVI or AlphaGenome Variant Impact, DeepMind variant effect prediction, or wants to prioritise or mechanistically interpret non-coding, regulatory, splicing, enhancer, promoter, or chromatin-accessibility effects of SNVs from a VCF, credible set, or region. Research use only; not a clinical tool.

Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates. Use for designing primer pairs, checking existing primers, exon-junction or isoform-specific assays, variant masking, cloning tails, multiplex compatibility, and interpreting Primer-BLAST results. Includes bounded local in-silico PCR and BLAST screening; distinguishes computational candidates from experimentally validated assays.

Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis. Used whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".

Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple indel through Folklore Clinical Variant Interpretation MCP. Used when a scientific agent must branch deterministically on resolved, ambiguous, not-found, invalid, unsupported, or unavailable variant outcomes; chain a resolved public variant into related literature or publication details; or preserve evidence provenance without accepting patient, phenotype, family, segregation, or private case data.