Biomedical Analysis Dispatch
xjtulyc/MedgeClaw
Routes bioinformatics, drug discovery, clinical and multi-omics tasks from a chat interface to Claude Code sessions running K-Dense scientific skills, with a live dashboard per task.
Official agent skill
Genomics Variant Interpretation
by aws-samples in aws-samples/amazon-bedrock-agents-healthcare-lifesciences
A skill your agent uses when interpreting genomic variants from VCF files, performing clinical variant classification using ClinVar/VEP annotations, analyzing allele frequencies against population…
Install Genomics Variant Interpretation
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences genomics-variant-interpretation --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genomics-variant-interpretation .claude/skills/genomics-variant-interpretation && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "genomics-variant-interpretation" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/genomics-variant-interpretation into .claude/skills/genomics-variant-interpretation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-variant-interpretation", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/genomics-variant-interpretationType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences genomics-variant-interpretation --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/genomics-variant-interpretation .agents/skills/genomics-variant-interpretation && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "genomics-variant-interpretation" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/genomics-variant-interpretation into .agents/skills/genomics-variant-interpretation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-variant-interpretation", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences genomics-variant-interpretation --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/genomics-variant-interpretation .cursor/skills/genomics-variant-interpretation && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "genomics-variant-interpretation" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/genomics-variant-interpretation into .cursor/skills/genomics-variant-interpretation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-variant-interpretation", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git --path skills/genomics-variant-interpretation--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences genomics-variant-interpretation --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/genomics-variant-interpretation .gemini/skills/genomics-variant-interpretation && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "genomics-variant-interpretation" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/genomics-variant-interpretation into .gemini/skills/genomics-variant-interpretation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-variant-interpretation", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences genomics-variant-interpretationInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/genomics-variant-interpretation .github/skills/genomics-variant-interpretation && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "genomics-variant-interpretation" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/genomics-variant-interpretation into .github/skills/genomics-variant-interpretation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-variant-interpretation", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences genomics-variant-interpretation --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/genomics-variant-interpretation .opencode/skills/genomics-variant-interpretation && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "genomics-variant-interpretation" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/genomics-variant-interpretation into .opencode/skills/genomics-variant-interpretation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-variant-interpretation", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
genomics-variant-interpretation- GitHub stars
- 274
- Token cost
- ~1.5k tokens
- SKILL.md length
- 426 words
- Files
- 3 (incl. scripts, references)
- Skills in repo
- 12
- Repo updated
- First seen
- Licence
- MIT-0
At a glance
A skill your agent uses when interpreting genomic variants from VCF files, performing clinical variant classification using ClinVar/VEP annotations, analyzing allele frequencies against population…
- Works in 5 steps: Select the appropriate analysis tool → Apply quality filtering → Interpret clinical significance → …
- Interpreting genomic variants from VCF files
- SKILL.md covers When to use this skill, Workflow: Clinical Variant…, Tool Reference and Data Architecture, plus 2 more sections
- Performing clinical variant classification using ClinVar/VEP annotations
What it does
Genomics Variant Interpretation is an agent skill from aws-samples/amazon-bedrock-agents-healthcare-lifesciences, published by the product's own GitHub organization. Use when interpreting genomic variants from VCF files, performing clinical variant classification using ClinVar/VEP annotations, analyzing allele frequencies against population data (1000 Genomes), or generating clinical reports for genetic counseling.
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts and reference files.
It sits in Research & Science, covering Bioinformatics and Clinical and healthcare research. The licence is MIT-0.
When your agent uses it
- Interpreting genomic variants from VCF files
- Performing clinical variant classification using ClinVar/VEP annotations
- Analyzing allele frequencies against population data (1000 Genomes)
- Generating clinical reports for genetic counseling
Example prompts
- “/genomics-variant-interpretation”
Workflow steps
5 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 9960565. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/, which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Genomics Variant Interpretation loads about 1.5k tokens when it runs. Until then it costs about 71 tokens; SKILL.md has 426 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from aws-samples/amazon-bedrock-agents-healthcare-lifesciences at commit 9960565, republished under its MIT-0 licence (© aws-samples). 426 words, ~1,483 tokens.
Download SKILL.mdSave it as
.claude/skills/genomics-variant-interpretation/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.- name
- genomics-variant-interpretation
- description
- Use when interpreting genomic variants from VCF files, performing clinical variant classification using ClinVar/VEP annotations, analyzing allele frequencies against population data (1000 Genomes), or generating clinical reports for genetic counseling.
Genomics Variant Interpretation
When to use this skill
- Interpret variants in specific genes (BRCA1/2, TP53, CYP2D6)
- Classify variant pathogenicity using ClinVar + VEP annotations
- Compare allele frequencies against population databases (1000 Genomes)
- Analyze a patient cohort for pharmacogenomic or cancer-risk variants
- Generate clinical-grade variant reports
Workflow: Clinical Variant Interpretation
Step 1: Select the appropriate analysis tool
| User question | Tool | Parameters |
|---|---|---|
| Variants in specific genes | query_variants_by_gene | gene_symbols, sample_ids |
| Chromosomal region analysis | query_variants_by_chromosome | chromosome, position_range |
| Rare variant discovery | analyze_allele_frequencies | frequency_threshold |
| Cohort comparison | compare_sample_variants | sample_ids (min 2) |
| Complex/custom questions | execute_dynamic_genomics_query | user_question |
Step 2: Apply quality filtering
All queries automatically enforce:
qual > 30(quality score threshold)PASSfilter status- Cardinality checks on VEP annotation arrays
These filters ensure only high-confidence variants enter clinical interpretation.
Step 3: Interpret clinical significance
Classification hierarchy (act on highest applicable):
| ClinVar Significance | VEP Impact | Action |
|---|---|---|
| Pathogenic | HIGH | Immediate clinical attention |
| Pathogenic | MODERATE | Clinical attention, confirm with functional data |
| Likely_pathogenic | HIGH | Strong candidate, recommend confirmatory testing |
| Likely_pathogenic | MODERATE | Monitor, include in report |
| Uncertain_significance (VUS) | HIGH | Flag for reassessment, research interest |
| VUS | MODERATE | Monitor, periodic reclassification |
| Benign / Likely_benign | Any | No clinical action |
Priority scoring (used in query results):
Pathogenic + HIGH impact = 10
Pathogenic + MODERATE = 9
Likely_pathogenic + HIGH = 8
Likely_pathogenic + MODERATE = 7
VUS + HIGH = 6
HIGH impact (no ClinVar) = 5
VUS + MODERATE = 4
All others = 1Step 4: Assess population frequency context
Use analyze_allele_frequencies with 1000 Genomes data:
| Frequency category | Threshold | Interpretation |
|---|---|---|
| Very Rare | < 0.001 (0.1%) | Potential novel pathogenic variant |
| Rare | < 0.01 (1%) | Candidate for rare disease |
| Uncommon | < 0.05 (5%) | May be population-specific |
| Common | >= 0.05 | Likely benign polymorphism |
Rule: Pathogenic variants for Mendelian diseases are almost always < 1% frequency.
Step 5: Generate clinical report
Structure: Patient ID, Gene, Variant (chr:pos:ref>alt), Consequence, Impact, ClinVar significance, Population frequency (1000G AF + rarity category), Associated disease (CLNDN), Clinical interpretation, Recommended follow-up.
Show full SKILL.md (159 more words)Show less
Tool Reference
query_variants_by_gene
Input: gene_symbols ("BRCA1,BRCA2,TP53"), sample_ids (optional), include_frequency (bool)
Output: Variants with VEP annotation, ClinVar significance, priority score
Use for: Targeted gene panels, cancer predisposition, pharmacogenomicsquery_variants_by_chromosome
Input: chromosome ("17"), sample_ids (optional), position_range ("32000000-33000000")
Output: All PASS variants in region with annotations
Use for: CNV analysis, specific loci investigation, regional patternsanalyze_allele_frequencies
Input: sample_ids (optional), frequency_threshold (default 0.01)
Output: Variants with rarity classification, quality tiers, 1000G comparison
Use for: Rare disease analysis, novel variant discovery, population geneticscompare_sample_variants
Input: sample_ids ("NA21135,NA21137" -- minimum 2)
Output: Per-sample summary: total variants, pathogenic count, impact distribution, quality metrics
Use for: Family studies, cohort stratification, trio analysisexecute_dynamic_genomics_query
Input: user_question (natural language), sample_ids (optional)
Output: Custom SQL generated and executed against HealthOmics stores
Use for: Complex questions not covered by specialized toolsData Architecture
Variant data lives in AWS HealthOmics stores queried via Athena:
- Variant Store (genomicsvariantstore): sample, position, alleles, quality, VEP annotations
- Annotation Store (genomicsannotationstore): ClinVar attributes (CLNSIG, CLNDN, GENEINFO)
Stores are joined on: contigname + start + referenceallele + alternatealleles[1]
VEP annotation fields: symbol, impact, consequence, biotype, sift_prediction, polyphen_prediction
ClinVar fields: CLNSIG, CLNDN, GENEINFO, CLNREVSTAT, RS, ALLELEID
Common Analysis Patterns
| Pattern | Genes | Filter | Action |
|---|---|---|---|
| Cancer predisposition | BRCA1, BRCA2, TP53, PALB2, CHEK2, ATM | Pathogenic/Likely_pathogenic | Genetic counseling referral |
| Pharmacogenomics | CYP2D6, CYP2C19, CYP2C9, DPYD, TPMT | Functional impact alleles | Medication dosing adjustment |
| Rare disease triage | All (frequency filter) | Very Rare + HIGH + not Benign | Candidate list for clinical review |
Conventions
- Lead reports with the most actionable finding first
- Include population frequency context for every pathogenic call
- Distinguish germline (inherited) from somatic (tumor) context
- For VUS: note classification may change with new evidence
- Never state a variant is definitively causal without functional evidence
- Include quality metrics (qual, depth) to assess confidence
© aws-samples, MIT-0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 2 other files (scripts, references) in skills/genomics-variant-interpretation of aws-samples/amazon-bedrock-agents-healthcare-lifesciences.
- SKILL.md
- references/.gitkeep
- scripts/.gitkeep
Open the folder on GitHubat commit 9960565
Compare with similar skills
Genomics Variant Interpretation next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Genomics Variant Interpretation this skillaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | — | ~1.5k | Automated safety check: Pass | MIT-0 | |
| Biomedical Analysis Dispatchxjtulyc/MedgeClaw | 617 | 1 repos | ~2k | Automated safety check: Pass | None | |
| PacsomaticK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~1.6k | Automated safety check: Pass | MIT | |
| Tooluniverse Precision Medicine Stratificationwu-yc/LabClaw | 1.1k | 2 repos | ~12k | Automated safety check: Pass | None | |
| Database Lookupmajiayu000/claude-skill-registry | 666 | 1 repos | ~7k | Automated safety check: Notes | MIT | |
| Biomedical Skillswentorai/research-plugins | 298 | 1 repos | ~827 | Automated safety check: Pass | MIT |
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Questions about Genomics Variant Interpretation
What does Genomics Variant Interpretation do?
A skill your agent uses when interpreting genomic variants from VCF files, performing clinical variant classification using ClinVar/VEP annotations, analyzing allele frequencies against population…. Genomics Variant Interpretation is an agent skill from aws-samples/amazon-bedrock-agents-healthcare-lifesciences, published by the product's own GitHub organization. Use when interpreting genomic variants from VCF files, performing clinical variant classification using ClinVar/VEP annotations, analyzing allele frequencies against population data (1000 Genomes), or generating clinical reports for genetic counseling.
When should I use Genomics Variant Interpretation?
Genomics Variant Interpretation fits situations like: interpreting genomic variants from VCF files; performing clinical variant classification using ClinVar/VEP annotations; analyzing allele frequencies against population data (1000 Genomes); generating clinical reports for genetic counseling.
How do I install Genomics Variant Interpretation in Claude Code?
Run `npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a claude-code`. Or copy the skill folder (skills/genomics-variant-interpretation in aws-samples/amazon-bedrock-agents-healthcare-lifesciences) into .claude/skills/genomics-variant-interpretation in your project. Claude Code loads it when a task matches its description.
How do I install Genomics Variant Interpretation in Codex?
Run `npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a codex`. Or copy the skill folder (skills/genomics-variant-interpretation in aws-samples/amazon-bedrock-agents-healthcare-lifesciences) into .agents/skills/genomics-variant-interpretation in your project. Codex loads it when a task matches its description.
Can I use Genomics Variant Interpretation in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill genomics-variant-interpretation -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/genomics-variant-interpretation, .gemini/skills/genomics-variant-interpretation, .github/skills/genomics-variant-interpretation and .opencode/skills/genomics-variant-interpretation in your project.
What does Genomics Variant Interpretation need to run?
SKILL.md names no scripts, command-line tools or credentials: Genomics Variant Interpretation is instructions for the agent only.
Does Genomics Variant Interpretation access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Genomics Variant Interpretation safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Genomics Variant Interpretation use?
Genomics Variant Interpretation is published under the MIT-0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Genomics Variant Interpretation use?
About 1.5k tokens (SKILL.md is roughly 5.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Genomics Variant Interpretation?
Skills that share tags, products or a category with Genomics Variant Interpretation: Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars), Pacsomatic (K-Dense-AI/scientific-agent-skills, 48k stars), Tooluniverse Precision Medicine Stratification (wu-yc/LabClaw, 1.1k stars) and Database Lookup (majiayu000/claude-skill-registry, 666 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Genomics Variant Interpretation?
aws-samples (a GitHub organization, an official publisher) maintains it in aws-samples/amazon-bedrock-agents-healthcare-lifesciences, which has 274 GitHub stars. The repository holds 12 skills in this directory. The repository was last updated on October 1, 2026.
Source: aws-samples/amazon-bedrock-agents-healthcare-lifesciences on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.