Single-trait GWAS for reproductive fitness in Drososphila melanogaster (Sussex LHM)

Code, data, logs, and graphs for GWAS on seperate-sex reproductive fitness in Drosophila melanogaster, Sussex LHM population sample. The shell script, code_drive_basic_gwas.sh, downloads input data files from the internet, drives Plink to select LD-independent SNPs, and then perform a genome-wide association test against female and male fitness, separately. Plink is also used to assign functions and gene names to SNPs. Bash/Unix code is used for formatting/compatibility adjustments, and also to add NCBI-dbSNP IDs to results. The shell script starts an R script that calculates expected p-values and FDR values based-on independent SNPs, plots diagnostic graphs, and outputs data to file. Explanations are provided in the code at each stage. A single R script for installing the packages used is provided. Remember to check software and package versions. See https://f1000research.com/articles/5-2644/v3 and http://www.sussex.ac.uk/lifesci/morrowlab/