genebass-gene-burden-skill

name: genebass-gene-burden-skill description: Submit compact Genebass gene burden requests for one Ensembl gene ID and one burden set. Use when a user wants concise Genebass PheWAS summaries

Operating rules

• Use scripts/genebass_gene_burden.py for all Genebass calls.
• This skill accepts one Ensembl gene ID per invocation.
• max_results is flexible; start around 25 for broad summaries and increase only if the user explicitly wants more associations.
• Re-run requests in long conversations instead of relying on older tool output.
• Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return raw JSON only if the user explicitly asks for machine-readable output.
• Supported burden sets are pLoF, missense|LC, and synonymous, with the aliases already handled by the script.
• If the user needs the full result set, increase max_results deliberately instead of dumping everything by default.

Input

• Read JSON from stdin as either a string Ensembl ID or an object.
• String form:
  • "ENSG00000173531"
• Object form:
  • {"ensembl_gene_id":"ENSG00000173531","burden_set":"pLoF","max_results":25}

Output

• Success returns ok, source, input metadata, gene, association counts, truncated, and compact associations.
• Failure returns ok=false with error.code and error.message.

Execution

echo '{"ensembl_gene_id":"ENSG00000173531","burden_set":"pLoF","max_results":25}' | python scripts/genebass_gene_burden.py

References

• No additional runtime references are required; keep the import package limited to this file and scripts/genebass_gene_burden.py.