Good progress: I generated a new VCF using GATK’s haploTypeCaller and was able to import the resulting variants into a data matrix. There were a few multi-allelic loci which I had to eliminate before I was able to use the variant_qc method. From there I was able to complete all of the examples from the Quality Control section of the 01-genome-wide-association tutorial with my data. Nice!
Sorghum is indeed diploid.