$ account statgen
Pheweb is a full-stack web application for building interactive PheWAS (Phenome-Wide Association Study) websites from GWAS summary statistics. It provides a command-line pipeline to ingest association files, annotate variants with rsIDs and genes, compute Manhattan and QQ plots, and generate a searchable, browsable web interface with LocusZoom region views, phenotype correlations, and top hits tables. The architecture is a Flask monolith with a JavaScript frontend using D3.js, jQuery, and Bootstrap. While the codebase is well-organized for its domain and includes some reusable components (e.g., a simple flat-file indexer and a CFFI matrix builder), it suffers from significant technical drift: outdated dependencies (Flask 1.1, jQuery 1.12, Bootstrap 3.3.7, D3 v5), deprecated Python patterns, and a successor project (PheWeb2) explicitly recommended in the README. The project is functionally complete but in maintenance mode, with limited test coverage and several known bugs documented in the changelog.