If you have only a single population, the linkage-based QTL mapping would be method of choice. If you have more than one population, and some other inbreds along these IRILs that are genotyped, GWAS would be better choice.

First, and the hardest step for linkage based mapping is to make a linkage map and eliminate poorly typed and redundant markers, as well as the ones failed to be assigned to any chromosome.

Excellent software for this purpose is R/qtl or R/qtl2 package with included vignettes