Methods supporting https://doi.org/10.7554/eLife.29593.001, "Natural variation in stochastic photoreceptor specification and color preference in Drosophila"
We performed a GWAS for the Rh4 ratio phenotype using simulated genotypes based on the original DGRP line phenotypes. A snakemake Snakefile to perform the entire analysis is provided. PLINK v1.90p 64-bit (25 Mar 2016) from bioconda was used. A conda environment file is provided.