annotating-variants
将原始变异转成可解读、可下游分析的注释记录，科研/临床常用。
通常处理敏感基因组数据，使用和共享时需合规保护隐私
对 VCF/rsID/HGVS 变异进行注释并规范化为 HGVS 表示，补充频率与预测信息。
把 VCF、rsID 或 HGVS 字符串规范化并注释，补充转录本映射、功能后果预测和 gnomAD 等人群频率信息，便于把基因变异与临床上下文关联。常用 Ensembl VEP、SnpEff、ANNOVAR 等无执照注释器，适合做变异解读、注释 VCF 或把变异数据接入临床文本分析。
▸ 展开 SKILL.md 英文原文
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and the clinical context OpenMed extracts. Use when the user wants to predict variant consequences, map HGVS to genomic coordinates, annotate a VCF, attach allele frequencies, or pair variants with phenotype/oncology context. Trigger keywords: VCF, HGVS, variant annotation, VEP, SnpEff, ANNOVAR, consequence, missense, gnomAD, allele frequency, GRCh38, rsID, transcript. Pairs adjacent to OpenMed: combine annotated variants with Genomics/Oncology entities and phenotype from openmed.analyze_text. Tools used are free; restricted clinical databases are user-supplied.
帮我安装这个 skill：https://raw.githubusercontent.com/maziyarpanahi/openmed/master/skills/annotating-variants/SKILL.mdcurl -fsSL "https://raw.githubusercontent.com/maziyarpanahi/openmed/master/skills/annotating-variants/SKILL.md"# Annotating variants & normalizing HGVS Turn raw genomic variants — VCF rows, rsIDs, or **HGVS** strings — into annotated, consequence-predicted records, and link them to the **clinical context** OpenMed extracts from text (genes, variants, oncology findings, phenotype). The workhorse for a quick, no-install annotation is the **Ensembl VEP REST API**; for scale, run **VEP**, **SnpEff**, or **ANNOVAR** offline. These annotators are **free and license-permissive**. Restricted clinical interpretation databases (e.g. licensed HGMD) are **user-supplied** — this skill sticks to open resources (Ensembl, gnomAD, ClinVar). ## When to use - You have a VCF / HGVS / rsID and need consequence predic