Methods and Scripts for 2 QTL papers on Mapping Grain Quality Traits in Sorghum
Boyles, R.E., Pfeiffer, B.K., Cooper, E.A. et al. Theor Appl Genet (2017) 130: 697. https://doi.org/10.1007/s00122-016-2844-6
Boyles, R.E., Pfeiffer, B.K., Cooper, E.A. et al. Crop Sci (2017) 57.
A repository of R scripts and instructions for calculating linkage disequilibrium with the R genetics package, and plotting the decay of LD.
A document giving detailed command lines used to create the final SAP SNP file with TASSEL 5.0
A repository of Perl scripts and instructions for performing various filtering steps and calculations with hapmap files created by TASSEL.
A repository with R scripts and instructions for finding and plotting recombination breakpoints in RIL populations.
A repository with R scripts and instructions for running GWAS with 2 different methods, including the GAPIT method used in this paper.