Search: "variants"

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.

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.

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.

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.