The snp chip GWAS results are output from RepeatABEL, and can be linked to the raw genotype data in the .tped file via comparing the scaffold:pos 
column in the result to the second column in the .tped file which includes the scaffold:position information. Note that 
each entry in the second column in the .tped file starts with a number (e.g., "1_"). Removing the number and the underscore 
from these entries will make these equivalent to the snpnames given in the GWAS results file... This can be done in R using the
colSplit funcation which is included in the reshape2 library.