Scripts and Instructions for the analyses in
Brenton, Z. W., Cooper, E. A., Myers, M. T., Boyles, R. E., Shakoor, N., Zielinski, K. J., … Kresovich, S. (2016). A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy. Genetics, 204(1), 21–33.
See our complete command lines for running the pipeline in the "TASSEL_BAP.md" file.
Refer to the Instructions and Scripts in the HapMap_Helpers respository to filter hapmap files for missing data and minor allele frequency.
Performed with
Refer to the instructions and scripts in the formatConversion repository to find the Perl scripts to convert between hapmap format and fastPHASE input/output format.
To run the program , you can also refer to programs within the formatConversion repository to convert the hapmap format to the STRUCTURE input format.
Instructions and code for the GAPIT pipeline can be found in the GWAS_Pipelines repository.
Instructions and code for using the R 'genetics' package to calculate linkage disequilibrium can be found in the LDanalysis repository. This includes a script for converting a hapmap file to the necessary input format, running the R package analysis automatically, and binning and plotting results.