Reference Data for GNExT Platform (1,000 Genomes Reference Data & Gene Annotations)

The GitHub repository DyHealthNet/gnext_reference_data provides scripts to generate the reference resources required for deploying an instance of the GNExT platform. Specifically, we describe the construction of a PLINK formatted reference panel from the 1000 Genomes Project Phase 3 dataset, which is used by MAGMA for linkage disequilibrium estimation. In addition, GNExT requires gene annotation resources for SNP to gene mapping; accordingly, the repository includes a script to derive the corresponding annotation file from any Ensembl GTF release. The reference sources produced by these scripts are deposited in this Zenodo, including PLINK files for GRCh37 and GRCh38 across five super populations as well as Ensembl protein-coding gene annotation files for GRCh37 and GRCh38 from Ensembl releases 114 and 115.