A repo with some genralized code for QTL mapping in maize using R/qtl
A link to a really nice book by Karl Broman and Saunak Sen on QTL mapping using R/qtl http://www.leg.ufpr.br/~eder/ebooksclub.org__A_Guide_to_QTL_Mapping_with_R_qtl__Statistics_for_Biology_and_Health_.pdf
The link to Karl Broman's website with some nice examples on QTL mapping (has examples of correct formatting of input data!) https://rqtl.org/
This repo includes code that was originally used to map the Tcb1-s and Ga1-s loci in maize. It has been generalized for other mapping cases in maize.
Input data (I think), contains the 'original' 1006 NAM markers. There are other NAM markers available that are more dense that may be worth trying out, see section below.
NAM_genos_mapping_20080103.txt
Taken from: http://datacommons.cyverse.org/browse/iplant/home/shared/panzea/genotypes/SNPs/NAM_map_and_genos-120731.zip
If you're feeling up for an adventure, try these markers: ~7k markers: http://datacommons.cyverse.org/browse/iplant/home/shared/panzea/genotypes/GBS/v23/NAM.GBSv23.imputedMarkers.0.2cm.zip
Merritt Burch