mjacksonhill/compile_hill_et_al._2022_bmc_plant_biology

GWAS COMputational PIpeLinE built on GAPIT

ComPile: GWAS COMputational PIpeLinE

The goal of providing these Supplemental Datasets is to:

1. Facilitate the generation of the files prerequisite to executing the COMPILE workflow
2. Allow reproduction of the results in the manuscript, and broadly of the entire COMPILE workflow
3. Provide working, interactive of COMPILE functionality for ease of adapting the system for other species and datasets.

Supplemental Dataset 1 is concerned with the generation of prerequisite files. Supplemental Dataset 2 is concerned with the execution of GWAS and the annotation of GWAS results. Supplemental Dataset 3 is concerned with the re-analysis of GWAS results using different parameters, as well as visualization of GWAS results.

Each supplemental dataset contains a WORKFLOW.txt file detailing the general usage of the scripts within, and SD2 contains an additional STUDY_DB_PREP.txt file detailing the origins of the files used in this study.

Each script within these datasets contains a section at the top identifying:

1. General purpose of the script
2. Folder architecture required to execute the script, including prerequisite, input, and output files
3. Information on how one might begin to customize the script for use with new datasets