Separate-sex GWAS for reproductive fitness in Drosophila melanogaster (Sussex LHM sample)

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 generates basic diagnostic graphs. This updated version differs from the first in that three large unconfirmed snRNA genes have been omitted to improve assignment of SNPs to genes.

See https://f1000research.com/articles/5-2644/v3 and http://www.sussex.ac.uk/lifesci/morrowlab/