A collection of scripts, command lines, and instructions for the analyses performed in
Boyles, R. E., E. A. Cooper, M. T. Myers, Z. Brenton, B. L. Rauh, G. P. Morris, and S. Kresovich. 2016. Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm. Plant Genome 9.
The complete set of command lines run to call SNPs with the TASSEL 5.0 pipeline.
A repository of perl scripts and instructions for performing various functions on HapMap files, including filtering for missing data and minor allele frequency, as used in this paper.
A repository of perl scripts and instructions for converting between various file formats, including between the hapmap format and the fastPHASE format, as well as hapmap and STRUCTURE formats.
Contains instructions and R code for running both the GAPIT and GEMMA programs as described in the paper.