An R script for simple gwassing.
Adapted from the work of researchers at NIAB.
Techniques here were used for MAGIC analysis of awning.
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.