LYNXgwas

Locus anaYsis and geNomic eXplorer — a local GWAS visualization platform.

Point it at your GWAS summary statistics and it identifies loci, recovers rsIDs, computes LD, runs fine-mapping (SuSiE, FINEMAP, COJO, coloc, GWAMA), and gives you an interactive Manhattan/LD/gene-track viewer per locus — all in your browser, entirely on your own machine. No data ever leaves your computer.

Screenshots

Home page — manage multiple GWAS projects, see status and locus/SNP counts at a glance:

Locus viewer — Manhattan plot, gene track, and LD triangle for a single locus:

Install

pip install lynxgwas

Requires a Java 11+ runtime on your machine (Adoptium is a good source if you don't have one).

Quick start

lynxgwas

This starts the local server and opens http://localhost:8765/ in your browser. On first run it will ask for (or offer to download) two things the pipeline needs:

• PLINK 1.9 — for LD computation and reference-panel subsetting (--plink <path> to skip the prompt)
• A GENCODE GFF3 annotation — for the gene track (--gff3 <path> to skip the prompt)

Both are remembered afterward. From the home page, use + New project to point LYNXgwas at your own GWAS summary statistics and walk through the setup wizard.

Features

• Automatic loci identification from GWAS summary stats (PLINK clumping)
• rsID recovery (local dbSNP + optional NCBI/gnomAD lookups)
• LD computation and pairwise LD triangles per locus
• Fine-mapping: SuSiE, FINEMAP, GCTA-COJO, coloc, GWAMA, and cross-ancestry SuSiEx
• Interactive Manhattan plot, gene track, and locus editing (resize/split/create) in the browser
• Per-locus and whole-genome PDF export; Excel export of all annotated SNPs
• Multi-project management from a single home page

Requirements

Documentation

Full architecture, Java package reference, API endpoints, and configuration keys: docs/ARCHITECTURE.md

License

MIT