varpubs is a command-line tool that automates retrieval and summarization of variant-associated biomedical literature to support faster variant interpretation in oncology.

Identifying treatment-relevant evidence for rare or poorly characterized mutations often requires reviewing large volumes of PubMed articles. varpubs streamlines this process by querying literature for variant-linked publications and generating concise, role-specific three-sentence summaries using a large language model (LLM). Optional LLM-based “judges” can score articles based on user given terms (e.g., therapy relevance) to prioritize relevant articles.

Variant-level summaries are written to a TSV file for direct use in clinical dashboards, molecular tumor boards, or downstream pipelines. A caching system stores previously generated summaries to reduce runtime in subsequent analyses.

pixi global install varpubs

conda install -c bioconda varpubs

varpubs deploy-db \
  --db-path pubmed.duckdb \
  --vcf-paths variants.vcf.gz other.vcf.gz \

varpubs summarize-variants \
  --db-path pubmed.duckdb \
  --vcf-path variants_annotated.vcf.gz \
  --llm-url https://your-llm-endpoint \
  --api-key $HF_TOKEN \
  --model medgemma-27b-it \
  --role physician \
  --cache cache.duckdb \
  --output summaries.tsv \
  --output-cache tmp_cache.duckdb

varpubs update-cache \
  --cache tmp_cache.duckdb \
  --output cache.duckdb

• Felix Wiegand
• Felix Mölder
• Hendrik Damm
• İlmay Taş
• Johannes Köster