POPSTAR: Poly/Oligogenic Phenotype Score Testing And Resampling

POPSTAR is a suite of tools to compute and manipulate 'polygenic' scores, such as are produced by genotype-phenotype association studies. POPSTAR's core functionality is similar to PLINK's --score command, but in addition POPSTAR includes modules to estimate the significance of scores by resampling, and convenience functions to automatically import scores from online GWAS databases.

Installation

Usage

POPSTAR operates on an allele dosage file (dosages) and polygenic trait specification file (PTS) to generate polygenic score outputs.

popstar [options] --dosages=samples.dosages --models=models.pts

The polygenic trait specification (PTS) file defines the polygenic scores to be calculated by POPSTAR. The ebi2pts.R script in utils/ is a simple script to automatically generate a PTS file from EBI GWAS database tables, available at https://www.ebi.ac.uk/gwas/docs/file-downloads.

Formats

Allele dosage file format (.dosages)

Polygenic trait specification file format (.pts)

Output format