Oct 2026· Zenodo (CERN European Organization for Nuclear Research)
Scientific Computing and Data Management
Abstract
Small VCF databases, one per cohort. Variants, genotypes, and samples live in either chDB (embedded ClickHouse) or DuckDB; gene and ClinVar annotations live in a sibling DuckDB file. A bundled Model Context Protocol server exposes a small set of tools so a language-model client can query the cohort in natural language and see the SQL it generated. Designed for the gap between bcftools/cyvcf2 (single-file, no persistence) and Hail/TileDB-VCF (cluster-scale). Atomic two-phase ingest with rollback, sparse-aware cohort allele-frequency math, parallel ingest with index-aware region splitting, and Arrow/Parquet as a public interchange format via db dump and db ingest-parquet.
Supporting data, adapters, predictions and code for the article *Low-Cost LoRA Fine-Tuning of Small Language Models for Multi-Step Arithmetic Reasoning* by Jake O'Grady, Asena Isik Gürhan, Chee Fong Ting and Effirul Ramlan (University of Galway). We generated 20,000 GSM8K-derived arithmetic problems with step-by-step s...
O'Grady, Jake, Gürhan, Asena Isik, Chee, Fong Ting et al.· Zenodo (CERN European Organi...· 465 citations
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