README.md

GWASSER

An R script for simple gwassing.

Adapted from the work of researchers at NIAB.

Techniques here were used for MAGIC analysis of awning.

Usage

optional arguments:
  -h, --help            show this help message and exit
  --gFile GFILE         Genotype File
  --pFile PFILE [PFILE ...]
                        Phenotype File
  --mFile MAP           Map File
  --phenos PHENOS [PHENOS ...]
                        Phenotypes to associate with SNPs
  --cov [COVS [COVS ...]]
                        Phenotypes to include as mixed effects
  --outDir OUTDIR       Folder to store output in.
  --noPlots             Skip making manhatten plot.
  --saveInter           Whether or not to save intermediate files.